Clean Gut by Alejandro Junger MD (2013): What to eat and foods to avoid

by Penny Hammond on June 24, 2013 · 88 comments

in Diets


Clean Gut - book by Alejandro Junger MDClean Eats by Alejandro JungerClean Gut (2013) is a plan to repair leaky gut and dysbiosis, to improve your general health –

  • 80% greens and vegetables, 20% protein and good fats
  • Repair your gut by avoiding difficult-to-digest foods including starches, beans, most fruits, dairy, grains, factory meats, sugars, alcohol, caffeine
  • Food combination recommendations
  • Add back gluten and dairy to test them

Below is a description of the food recommendations in the book. There’s a lot more discussed in the book, which is a successor to the bestselling Clean.
Get a copy of Clean Gut for details of why a healthy gut is vital to your health, and recipes.

Get a copy of Clean Eats for over 200 recipes.

The reasoning behind Clean Gut

The book argues that what we call diseases are really just different forms of survival mechanisms for our body.  Before chronic disease comes systemic inflammation. But before systemic inflammation comes gut dysfunction. Gut damage from leaky gut (hyperpermeability) and dysbiosis  allow toxins to enter the body and cause havoc. This book discusses how to heal the gut and intestinal flora to improve your general health.

Clean Gut diet plan – food list

There are general Clean Gut diet guidelines for phases 1 and 2, and specific guidelines for each:

Phase 1 – 21 days – drink a liquid breakfast and eat meals from the Clean Gut diet, as well as taking recommended supplements and practicing specific activities to enhance the process of gut repair

Phase 2 – 7 days – reintroduce foods into your diet over the course of a week, which will allow you to identify the foods that do not promote long-term gut health

Also guidelines for testing triggers and for a lifetime diet

Clean Gut general guidelines

Eat  |  Avoid

Clean Gut foods to eat during the program – general – “The Clean Gut Diet”

  • Fill 80% of your plate with greens and vegetables (raw, steamed, baked, cooked) and 20% with protein and good fats (meat, fish, avocado, etc.)
  • Stop eating when you are 80% full – this will help your body digest more easily
  • Daily protocol
    • First thing in the morning, have a glass of water with half a squeezed lemon
    • For breakfast, have a green shake plus supplements. There are recipes in the book and at Ideally you should vary the shakes. If you have nut allergies, use sunflower seed butter or coconut manna instead, or omit them
    • For lunch, have a meal from the Clean Gut diet (guidelines aren’t clear)
    • For dinner, have a meal from the recipes, consisting of an entrée-size salad
    • There’s also a supplement protocol to go with these meals
  • Combine mindfully for better digestion
    • Pair vegetables and greens with animal protein (fish, meat, eggs)
    • Pair vegetables and greens with vegetable protein (e.g. lentils, quinoa)
    • Don’t pair animal protein and vegetable protein – e.g. don’t pair chicken and quinoa, instead eat chicken and veggies or quinoa and veggies
  • Vegetables
    • Whole vegetables, preferably organic and local
    • Raw, steamed, sautéed, juiced, or roasted
    • Acorn squash, arugula, asparagus, avocado, baby greens, bean sprouts, bok choy, broccoli, butternut squash, cabbage, napa cabbage, carrots, cauliflower, celery, chard, cucumbers, delicata squash, fennel, kabocha squash, kale, kohlrabi, leeks, lettuce, mushrooms, onions, parsnips, green peas, bell peppers, hot peppers, pumpkin, radish, scallions, shallot, snow peas, spaghetti squash, spinach, tomato, yellow squash, zucchini, etc.
    • Squash, tomatoes, etc.
    • Seaweed and water vegetables – e.g. dulse, nori, spirulina powder
  • Fruit
    • Only fresh and frozen berries, lemons, and limes
    • Preferably organic and local
  • Dairy substitutes
    • Unsweetened and free of xanthan gum
    • Hemp milk
    • Nut milks – almond milk, hazelnut milk, walnut milk, etc.
    • Coconut milk, coconut water, coconut oil, coconut butter – unsweetened, no added flavor, organic when possible. (You can use canned coconut milk, but it’s very rich and some brands may have additives. Read the ingredients and, when in doubt, make your own. You can also use coconut milk in a carton from the health-food or grocery store.)
  • Eggs
    • Organic or pasture-raised eggs
  • Grains
    • Quinoa – go easy on these and lentils, only a side serving a day
  • Meat and fish
    • Fish – Fresh or water-packed cold-water fish – anchovies, cod, halibut, kippers, mackerel, pike, salmon, sardines, tuna, trout, etc.
    • Wild game – bison, elk, pheasant, rabbit, venison, etc.
    • Meats – lamb, small amounts of grass-fed beef. Preferably organic, pasture-raised, and grass-fed – check out for a state-by-state listing of organic and grass-fed animal products
    • Poultry – organic chicken, duck, organic turkey, free-range sugar-free turkey bacon
  • Vegetable proteins
    • Legumes – split peas, lentils – go easy on these and quinoa, only a side serving a day (note – soy foods such as tofu are not permitted)
    • Bee pollen
    • Spirulina, blue-green algae
  • Nuts and seeds
    • Go easy on nuts – only a handful a day
    • Raw varieties free of preservatives, salt and sugar
    • Nuts – almonds, brazil nuts, cashews, coconut, macadamia nuts, pecans, pistachios, walnuts, etc. (No peanuts)
    • Seeds – chia seeds, hemp seeds, sesame seeds, sunflower seeds, etc.
    • Nut and seed butters – almond butter, cashew butter, tahini, etc. – unsweetened, unsalted, raw or dry-roasted, organic when possible
    • Nut and seed flours and meals – e.g. almond flour, flax meal
  • Fats and oils
    • Look for organic expeller and cold-pressed, unrefined oils
    • Almond oil, avocado oil, coconut oil, flax oil, extra-virgin olive oil, pumpkin oil, safflower oil, sesame oil, sunflower oil, walnut oil
    • Avocados
  • Fermented foods
    • Kimchi, sauerkraut, etc.
  • Drinks
    • Filtered, seltzer, and mineral waters
    • Green and white teas
    • Herbal teas
    • Yerba maté
    • Coconut water
    • Green juices
  • Sweeteners
    • Stevia, xylitol, Lakanto
  • Condiments and pantry
    • All herbs , including bay leaf, basil, chives, cilantro, dill, mint, parsley, rosemary, sage, thyme
    • All spices, including cardamom, cayenne, cinnamon, cumin, curry powder, ginger, lemongrass, nutmeg, paprika, red pepper flakes
    • Black pepper, free-range or organic broth, capers, raw carob, raw chocolate/cacao (dairy- and sugar-free), coconut liquid aminos, fish sauce (Red Boat brand), unsweetened ketchup, miso, stone-ground mustard, nama shoyu, olives, sea salt, wheat-free tamari, vinegar
    • Plant-based protein powder – rice, hemp, or pea based, no soy
    • Nutritional yeast

Clean Gut foods to avoid during the program – general

  • Vegetables
    • Beets, corn, potatoes, sweet potatoes, yams
    • Creamed vegetables
  • Fruit
    • All fruits except berries, lemon and lime
    • Fruit juice
  • Dairy (note – dairy will be tested in phase 2)
    • All milk products – butter, cheese, cottage cheese, cream, ice cream, milk, yogurt
    • Nondairy creamers
  • Grains (note – gluten will be tested in phase 2)
    • All gluten-containing grains, including barley, rye, spelt, triticale, wheat
    • Other grains and pseudo-grains, including amaranth, buckwheat, kamut, millet, oats, rice – even if gluten-free
  • Meat and fish
    • Factory-farmed meats
    • Processed meats – canned meats, cold cuts, frankfurters/hot dogs
  • Vegetable proteins
    • All beans (not quite clear how you demark between beans, which aren’t allowed, and lentils and split peas, which are – for example, are black-eyed peas okay?)
    • Soybean products, including tofu, soy milk, edamame, soy-based ice-creams,  soy sauce and soybean oil in processed foods
  • Nuts and seeds
    • Peanuts and peanut butter
  • Fats and oils
    • Butter, canola oil, margarine, processed oils, shortening
    • Mayonnaise, salad dressings, and spreads
  • Drinks
    • Alcohol
    • Coffee and caffeinated beverages
    • Soda pop and soft drinks
    • Fruit juices
  • Sweeteners
    • All processed sugar
    • Refined sugar – brown sugar, high-fructose corn syrup HFCS, white sugar
    • Agave nectar, evaporated cane juice, honey, maple syrup
    • Juice concentrates
    • Equal, Splenda, Sweet’N Low
  • Condiments and pantry
    • Regular chocolate (with dairy and sugar)
    • Barbecue sauce, chutney, ketchup, relish, traditional soy sauce, teriyaki sauce
    • Protein powder – soy based
  • Foods with preservatives, dyes, MSG

Clean Gut program phase 1 foods

This phase lasts for 21 days

Some foods, like beans and certain fruits, are excluded because they are difficult to digest or high in sugar, even though they are the staple of most healthy diets. Once you’ve completed the Clean Gut program, they can be reintroduced into your regular diet

Clean Gut phase 1 foods to eat

Clean Gut phase 1 foods to avoid

Clean Gut phase 2 – reintroduction

The reintroduction process is the last stage of the Clean Gut program, on days 22-28. While staying on the Clean Gut diet, reintroduce gluten and dairy over seven days. The purpose of the process is to identify your toxic triggers – foods that cause inflammation, acidity, irritation, or indigestion; also allergic reactions, food sensitivities, autoimmune reactions, mood swings, bloating, fatigue.

Gluten and dairy are the most common toxic triggers. Others are processed sugar, caffeine, and alcohol

Clean Gut phase 2 – foods to eat

  • Keep a journal to record any reactions you might have to the foods you reintroduce – anything that happens shortly after eating the food, energy levels, bowel movements, sleep, emotions
  • On the first and second days (days 22 and 23), eat gluten 2-3 times a day for two days, as well as general Clean Gut diet Foods to Eat (above). Don’t include dairy or other excluded items yet
  • On the third and fourth days (days 24 and 25), eat from the Clean Gut diet Foods to Eat (above), without any gluten
  • On the fifth and sixth day (days 26 and 27), eat simple dairy foods (e.g. milk, cheese) 2-3 times a day for two days, as well as general Clean Gut diet Foods to Eat (above). Don’t include gluten and don’t include other excluded items yet – so stay away from cereal, ice cream, and baked goods at the moment
  • On day 28, reflect on how your reactions to the reintroduced foods have been. If you had no reaction, you can keep it in your diet. If you had a mild reaction, rotate your choices of foods so that you don’t eat the irritating ones more than once a week. If you had a strong reaction, remove the food from your diet

Clean Gut phase 2 – foods to avoid

Potentially healthy or toxic foods to test after phase 2

Once you’ve finished the program, you can test other foods apart from gluten and dairy. Other foods that are commonly healthy for some and toxic triggers for others include:

  • Corn
  • Eggs
  • Soy
  • Red meat
  • Nightshade vegetables (potatoes, tomatoes, peppers, eggplant)

As you’ve been avoiding corn and soy, you can test it at the end of the program. If you want to test eggs, red meat, and nightshade vegetables, avoid them for say 2-3 weeks and then reintroduce them for two days, one at a time while eating only Clean Diet foods, to find out your reaction.

Lifetime diet

  • Fill 80% of your plate with greens and vegetables (raw, steamed, baked, cooked) and 20% with protein and good fats (meat, fish, avocado, etc.)
  • Stop eating when you are 80% full – this will help your body digest more easily
  • The Big Three – processed sugar, caffeine, and alcohol – remove dependency
    • Crowd out – eat good quantities of healthy food each day so you have less room for these foods
    • Pulse out – remove them from your diet for a period of time, so you can feel and remind yourself of the full effects. Do this regularly, for one week or one month
    • When you do eat these foods, enjoy them, and be aware of the present moment with each bite or sip
  • General food guidelines
    • Fruits and vegetables – purchase organic or chemical-free fruits and vegetables
    • Meat – purchase organic, pasture-raised, and grass-fed
    • Fish – purchase smaller, cold-water fish, such as listed above in the general what to eat guidelines
    • Eggs – purchase organic, free-range, and pasture-raised eggs
    • Grains – If you’ve reintroduced grains and found that they work for you, consider including nongluten grains in your diet, such as quinoa, millet, buckwheat, and rice
    • Oils and fats – look for organic expeller and cold-pressed, unrefined oils. Oils such as lard, coconut oil, and ghee are higher in saturated fats and better for high-temperature cooking. Olive oil is good for medium-temperature cooking but is best used in salad dressings or as a condiment. Nut and seed oils should not be used for cooking, instead use them in cold preparations
    • Nuts and seeds – look for raw varieties free of preservatives and sugar
  • Alternative eating habits to try
    • If you typically eat meat at most meals, take one weekend to go vegetarian. Then try it for one week. See how your body reacts
    • Once every month, for 2-4 days, go completely grain-free, both gluten and nongluten varieties. Or try removing grain for 2 weeks to see how you react
    • Try soaking grains overnight before cooking will make them easier to digest
    • Beans, lentils, and legumes can be difficult for many people to digest. Try soaking them first overnight to see if they’re any easier to digest
    • Nuts and seeds can often be difficult to digest – soaking them for a few hours can help. If you feel heavy after eating them, reduce the amount you include in your diet. If you frequently snack on nuts and seeds, try reducing your quantity and frequency to one handful every other day, and see if this improves your digestion
    • Try using coconut oil for one week – cook with it, use it as a skin moisturizer, and add it to your shakes and recipes
    • Try removing corn and soy for two weeks
    • Try adding probiotics – a cup of raw, unpasteurized fermented vegetables, kimchi, or sauerkraut each day to your dinner for a week. Or add low-sugar probiotic drinks. Also add small amounts of kefir made from goat’s milk or cow’s milk if dairy is not a trigger food for you
    • Try adding 1-2 servings a day of a fresh green juice or green smoothie for two weeks
  • Mind your food combinations and don’t food bomb
    • A food bomb results from mixing too many different types of food together in one meal, and often happens on holidays. Each type of food requires different enzymes in order to be digested, so mixing too many together at once causes poor digestion and creates fatigue
    • Eat nonstarchy vegetables and leafy greens with animal protein, grains, rice, legumes, and starchy vegetables
    • Avoid eating animal protein with grains, rice, or legumes
    • Eat fruit alone
  • Have a shake a day from the Clean Gut shake recipes

Health benefits claimed in Clean Gut

The diet in this book claims to reduce the risks for: abdominal distention, aches and pains, food allergies, seasonal allergies, arthritis, asthma, autoimmune diseases, back pain, bad breath, bloating, body odor, cancer, cholecystitis, constipation, cramping, Crohn’s disease, depression, diabetes, diverticulitis, dysbiosis, eczema, gas, gastroesophageal reflux GERD, gluten sensitivity, Hashimoto’s thyroiditis, heart disease, hemorrhoids, hormonal imbalances, infertility, inflammatory bowel disease IBD, insomnia, iritis, irritable bowel syndrome IBS, lack of libido, leaky gut / hyperpermeability, mood swings, peptic ulcers, skin lesions, tiredness/fatigue, ulcerative colitis, yeast overgrowth; also premature aging

As always, this is not intended to be a replacement for professional medical diagnosis or treatment for a medical condition. Consult your doctor before starting a new diet. This page describes what the authors of the diet recommend – Chewfo is describing the diet only, not endorsing it.

Get a copy of Clean Gut for details of why a healthy gut is vital to your health, and recipes

Buy now from Amazon Dietary cleanse/detox
Get a copy of Clean for a more general detox, recommended before this program.

Buy now from Amazon General cleanse/detox
Get a copy of Clean Eats for over 200 recipes

Buy now from Amazon Cleanse/detox recipes
Also see for recommended supplements and recipes.

How has this diet helped you? Please add a comment below.


{ 88 comments… read them below or add one }

Ana T Rodriguez October 2, 2013 at 9:06 am

I am doing the clean gut diet at the present moment, and I have one question the book said that we should eat 5 time a day but I don’t see what are the other food we can eat, the book only mention shakes lunch dinner but no shacks. I am using the nuts and berries as snack. I that ok?


Penny Hammond October 2, 2013 at 7:33 pm

Generally Dr. Junger refers to having 3 meals a day, some of which may be liquid meals. Could you let me know where in the book it says to eat 5 times a day?


Joyce October 5, 2013 at 12:08 pm

I would like to start this protocol but I have issues with most protein foods except beef, bison and elk meats. Ie. no nuts, soy, chicken, eggs, beans,etc. I have had reactions to “green”supplements ‘ probiotics and even magnesium. I’m afraid of taking pills of any kind as I react to many of them, esp. Antibiotics. Should I take it slow and introduce these supplements one at a time until I see how things go?


Penny Hammond October 6, 2013 at 8:26 am

Sorry to hear about all your reactions. It sounds like you really need this diet to heal your gut!

This diet is asks you to eat mostly vegetables, 80% of your diet. For protein, it asks you to limit some of the foods you react to, like nuts, and avoid others, like soy and beans. If beef, bison, and elk work for you, use them as your proteins.

Dr. Junger points out that each person is different so the best supplement programs will be tailored to your specific history and nutritional needs (p. 132). He recommends getting tested to see which supplements you need – if you’re extremely reactive it may be worth doing this to allow you to concentrate on mending nutritional gaps so your gut can heal faster.
I concentrate on the food part of diets, rather than supplements, but for the supplements Dr. Junger lists on p.132 (which he says most people need), introducing them one at a time sounds like a good idea in your case.


Darlene May October 6, 2013 at 9:03 am

I have been on Dr. Junger’s program for one week now and have lost 9 lbs. I am absolutely thrilled with these results. I am not hungry all the time and I don’t have the food cravings in the evening. I believe this is the result of the elimination of sugar. I am having so much fun trying new recipes and have inspired my husband to join me. I feel fantastic both physically and mentally. What I plan to do is stick to phase 1 and skip phase 2. I don’t want to reintroduce food to identify my toxic triggers – foods that cause inflammation, acidity, irritation, or indigestion; also allergic reactions, food sensitivities, autoimmune reactions, mood swings, bloating, fatigue. I don’t ever want to feel any of that again. Thank you Dr. Junger for showing me the way.


Penny Hammond October 6, 2013 at 9:20 am

How wonderful that the results have been so good for you!

While I understand that it’s an incredible relief to get rid of your symptoms, I suggest that you consider reintroducing foods to find out which ones are your personal toxic triggers. They aren’t the same for everybody. Eating just the phase 1 foods can be very limiting, especially socially, and you may be avoiding foods that are potentially healthful for you. It can also be empowering to know exactly which foods are your own personal toxic triggers – that allows you to concentrate your vigilance on your true enemies, rather than watching out for a very large group of foods you’re avoiding on phase 1.


Darlene May October 7, 2013 at 10:52 am

Thank you so much for your prompt reply. I will try introducing some foods, but will eat gluten free. I do have sugar issues and without the starches, I am finding things so much easier. I am scheduled for blood work next week and then I will find out from the doctor if there is any improvement.


TJ Eiford November 18, 2013 at 11:26 am

What about whey protein isolate?


Penny Hammond November 18, 2013 at 5:56 pm

Whey protein isolate is a dairy food, which should be avoided in phase 1 of this diet, and reintroduced only if dairy has been tested and passed.
As it’s highly processed, it’s possible that this could cause issues – this diet recommends eating “real” foods.


Gloria December 8, 2013 at 9:17 pm

I have problems with excessive belching after eating, I never know for sure the triggers food since it happen with the same foods and sometimes it doen’t. Vegetables might be triggers, is better rosted or cooked than raw?


Penny Hammond December 15, 2013 at 9:38 am

Cooked vegetables may give you less belching than raw, as they’re often easier to digest. But the author of this diet suggests eating raw vegetables as well as cooked.
Try chewing your food well, as this makes it easier for your digestive system to work on foods, and means you’re eating more slowly and possibly swallowing less air. Also try avoiding carbonated drinks.


Kim January 9, 2014 at 12:10 pm

I tried starting my program today and I am already so discouraged. I threw up the shake I made, creamy blueberry and I can’t seem to figure out why I am the only one to comment on the this? I have never tasted anything this awful in my life. I tried so hard to eat it. I am desperate to fix my health issues, but I don’t know what to do now. Any advice is appreciated. Thanks.


Penny Hammond January 9, 2014 at 6:47 pm

Sorry to hear that.
What didn’t you like in the shake – the texture/thickness, or the flavor?
Thickness – try adding more liquid
Taste – try one of the other recipes (look to see if you like all the ingredients), or add an ingredient which you like the taste of (e.g. cocoa powder) that’s in another shake recipe, or substitute an ingredient that’s in another recipe, e.g. coconut milk instead of almond milk.
You could also try drinking it slightly warm.

Keep in mind that Dr. Junger suggests you vary the shakes so you’re not having the same foods all the time – try to find a few that you like.


Alison August 21, 2014 at 12:04 pm

Hi Kim, my daughter just called me with the same problem. I suspect that there’s a typo in the recipe. I think that the 1.5 cups of shredded coconut should really be coconut water or coconut milk. Hope you didn’t give up on the diet because of this.


Anna January 12, 2014 at 6:06 pm

Hi, I just read the book. Maybe it just went totally over my head, but what on earth are we supposed to do for lunch and dinner? I get the supplement protocol. Can anyone explain:

For lunch, have a meal from the Clean Gut diet (guidelines aren’t clear) *****
For dinner, have a meal from the recipes, consisting of an entrée-size salad *****

For lunch, the guidelines AREN’T clear. I see the recipe section… are we supposed to just pick a recipe and have that? Where does the 80/20 come in?

For dinner, have a meal from the recipes and make it INTO an entree-sized salad? Or, have a recipe from the recipe section WITH a salad? I am so, so very confused.

Can anyone clarify this please? Thanks!


Penny Hammond January 13, 2014 at 10:13 am

In phase 1:

Lunch should be “A meal from the Clean Gut Diet” (p.98) – this is what’s listed in the general “what to eat” section above – following the 80-20 rule, eating only permitted foods, and combining foods using the guidelines of which foods should be eaten together.
As this doesn’t say you have to follow the recipes, you get a certain amount of flexibility in what to eat. Have a look at the recipe section – if you want to eat something from the recipes that meets these guidelines, go ahead, or you can create your own meal from the guidelines.
The recipes in the book should all contain only permitted foods and combinations – it’s up to you to keep an eye out for having 80% of your plate filled with greens and vegetables.

Dinner should be “A meal from the ‘Recipes’ section consisting of an entrée-size salad, plus supplements.” (p.98)
It looks like you should be picking one of the salad recipes (pages 203-209), but that’s a very limited selection, only 7 salads. My assumption looking at the description and recipes is that you should have a meal that’s mainly raw salad, but that can contain a small amount of easily-digested protein such as salmon or chicken. If you want to go outside the strict guidelines of following the recipes section, you could use the salad recipes as guidance to creating new salads that meet the “what to eat” requirements.

In phase 2:
Follow the guidelines above for lunch and dinner, adding foods that you’re reintroducing.

Hope that helps, let me know if anything isn’t clear.


Chuckwalla January 12, 2014 at 10:48 pm

Is tofu an acceptable food during the 21 day cleanse? It seems that it would fall into the vegetable protein category, but soy products were on the foods to avoid list.


Penny Hammond January 13, 2014 at 10:18 am

You’re right, it’s a vegetable protein but Dr. Junger says to avoid soy products – so it’s not an acceptable food.
For an explanation, see


Cathy P January 18, 2014 at 4:59 pm

Just wondering why fruits other than berries are not allowed during the 21 day cleanse. Also, are strawberries okay? They are not mentioned in any of the recipes so I’m unsure. Thanks!


Penny Hammond January 19, 2014 at 12:01 pm

Dr. Junger says “if you have an overgrowth of yeast, a frequent situation after antibiotic use, you may be throwing logs onto the fire. The sugar in fruit is on the list of a yeast’s favorite desserts.”
Berries, lemons, and limes are allowed because they’re low-sugar. Other fruits are excluded during the cleanse to reduce yeast overgrowth.

The only berry listed in the book are blueberries. Strawberries are usually considered a berry, and they’re not listed as “don’t eat”, so I assume you could eat them in moderation on this diet.


Lucy January 21, 2014 at 9:22 pm

I love the logic behind this program. Fix the gut and you solve a lot of problems. I am in week 2 and feel wonderful. I am also finding it easy to adhere to. But sometimes, I wonder if this book was quickly thrown together. I agree with a recent poster — the blueberry shake is inedible. It must be a mistake. And the shake options are very limited, esp. since Dr. Junger asks that you drink a green shake every morning. I’ve been drinking the shake with spinach, avocado, cashews and I’m totally over it. Wish there were more options.


Jen January 28, 2014 at 3:14 pm

This book was a life changer for me! I found that my primary migraine trigger is gluten, and dairy is also a headache trigger. I have completely eliminated them, permanently, from my diet. I believe 100% that leaky gut exists and is the source of more problems than I could have imagined. Had I not been so desperate to cure my headaches (I had a headache every minute of every day for three months with 2-3 migraines a week when I reached my desperation point), I would have never tried it – because I don’t ever have issues with my stomach, such as an upset stomach. Luckily, I found a holistic doctor, who explained leaky gut to me. I took it upon myself to learn more and bought the book. I did the strict 21 day cleanse even though (in all honesty) I didn’t like the shakes. Like some other posters, I drank the same one every day. I was sick of it by the end, but I toughed it out. I couldn’t tolerate the spirulina (headache!), but I did well with spinach. I also had some difficulty with a couple of the supplements and couldn’t take a few of them.

I guess my point with all of this is, try as best you can to get through the 21 day cleanse, as written, but you also have to do what works for your body. Try to do it as closely as you can. If your body won’t tolerate something, that’s one thing, but if your tastebuds are giving you issues, push through…it’ll be worth it! My migraines are GONE. My headaches are SIGNIFICANTLY reduced. Most of the time, I am headache-free, but I am still getting one a day (working on finding the trigger). I have decided to stay gluten-free, dairy-free, mostly grain-free and refined sugar-free. I am trying to stay with the correct food combinations as well. I don’t miss any of the foods I have elminated because the other option is….headache!

I have three friends now reading the book and their jaws dropped, as mine did, when they learned how it all comes down to your gut! :)


Penny Hammond January 29, 2014 at 7:34 am

Wow, what a relief that must be!

For your only remaining headache, look at habits and situations that may be triggering it – which could be environmental, food, or stress. Dr. Junger covers environmental and other other toxic factors in his earlier book, Clean.


Shannon February 23, 2014 at 8:44 am

Are dates and date syrup acceptable snacks and/or sweeteners during the Clean Gut cleanse?


Penny Hammond February 23, 2014 at 10:31 am

Dates are fruits, and the only fruits allowed in the cleanse are fresh and frozen berries, lemons, and limes. Any other fruits, including dates, and any caloric sweeteners, including date syrup, are not to be eaten in phase 1 or phase 2.


Deborah February 24, 2014 at 4:31 pm

I will start the 21 day gut cleanse 1 march. Is marmite permitted?


Penny Hammond February 24, 2014 at 9:29 pm

The book talks about how “viruses, parasites, yeast, and pathogenic bacteria—or the lack of good bacteria, are associated with many more problems than we ever thought” (p.42). Many cleanses ask you to exclude yeast completely.
There are a number of recipes in the book which contain nutritional yeast, but that’s a deactivated yeast. The main ingredient in Marmite is yeast extract – but I can’t find any clear guidance on whether it’s active or not.
So… maybe try not to have Marmite during phase 1 or phase 2, but reintroduce it after phase 2.


Marla Sloan February 26, 2014 at 12:10 pm

Why are eggs included in the clean gut program and not in the clean program? In the clean program we were told not to eat eggs in phase 1. Why the change?


Penny Hammond February 26, 2014 at 6:19 pm

Dr. Junger lists eggs as a possible allergic or toxic trigger in Clean and Clean Gut. He also lists a number of other foods as not to eat in Clean but okay in Clean Gut (including chicken and meat). Generally, it looks like he’s assuming you’ve already followed Clean and already know your triggers – and avoiding them. Also, he’s advising eating pastured eggs and meat, which may have different properties than factory-raised equivalents.
It wouldn’t be the first time a diet writer has changed their position over time as they learn more. But it could just be based on the assumption that you’ve already worked through the basic Clean and are ready for the next steps.


Adrian April 9, 2014 at 2:10 am

How can you and the author possibly assume one would have read the clean book before reading clean gut? That’s absurd and would want my money back. I’ve been following this program to the T for the last 28 days, reintroducing foods, etc, and haven’t found a significant change with any of my auto immune problems (I have a disease called dermatomyositis). I’ve spent almost 3000 dollars on food and supplements, changing everything out for organic and clean foods/spices, u name it. I’m going to continue testing foods, but even the program in itself, the foods it tells you to eat, u may have a food allergy to those as well!


Penny Hammond April 10, 2014 at 9:56 am

Clean Gut only covers food; there are often environmental factors which can trigger health conditions which is why Clean Gut won’t necessarily be effective on its own.

You’re right, the program may not work for people who have allergies or intolerances to the recommended foods – however, these are foods that people tend not to be sensitive to.
If you’re really interested in detecting your food allergies/intolerances in case it’s food rather than environment that’s causing your autoimmune problem, have a look at Food Allergies and Food Intolerance by Jonathan Brostoff – I used it many years ago to discover my own intolerances, it’s not exactly easy to do (especially if you tend to eat with other people) and it can take a while to test thoroughly, but it can really help pinpoint unusual triggers.


Sarah Aspinall February 26, 2014 at 4:50 pm

I have started the 21 day cleanse in the clean book. So far so good. The creamy blueberry shake on page 248 was impossible to make. I have a Vitamix. Is it 1.5 cups coconut or coconut milk? It says coconut but there is no liquid so I added water to be able to mix it. Was that a typo?
Also is the clean gut book much different? I have both. Should one do the clean cleanse first then the clean gut or what is suggested. Thank You
Looking forward to seeing what happens on the cleanse.


Penny Hammond February 26, 2014 at 6:12 pm

There’s nothing in Dr. Junger’s website to show errata in the book, but it sounds like that’s one of them (it was also pointed out by a reviewer on Amazon). Looking at the ingredients, that would make an extremely solid shake! You could try with coconut milk or coconut water, similar to the other recipes.

The author suggests trying Clean first – it has much more than just dietary advice, it claims to help you to reduce toxins in your whole environment. Clean gut is the “advanced” course focusing on diet alone.

Good luck with the cleanse!


Grace March 3, 2014 at 10:52 am

Does it matter what your blood type is?


Penny Hammond March 3, 2014 at 11:45 am

This book doesn’t talk about blood types at all.

The most popular book on diet and blood types is Eat Right 4 Your Type by Dr. Peter D’Adamo.


Ericca March 6, 2014 at 11:12 am

I am a vegetarian but I know I eat way to many processed foods and that it’s causing health issues. My only question is can you get sufficient protein when eating only a side of quinoa, lentils or split peas per day? Thanks so much for a great synopsis of the book and great responses to the questions people have asked here.


Penny Hammond March 6, 2014 at 12:19 pm

If you can eat eggs, they’re allowed on this diet (organic or pasture-raised).
Bee pollen, spirulina, and blue-green algae are also listed as vegetarian proteins, as are vegetarian protein powders (rice protein powder, hemp protein powder, and pea based protein powder).
Don’t forget that nuts and seeds contain protein as well.


Angelina March 10, 2014 at 10:13 am

I am hoping to start this programme in a weeks time. However I am really going to struggle with having a meal for lunch. So I am going to have to have a shake for lunch and then the meal for dinner. I know this is not the programme but it’s the only way I’m going to be able to do it. Will it still have the same health benefits? Thanks


Penny Hammond March 11, 2014 at 6:04 pm

That’s probably fine – I can’t see anything in the book about letting your digestive system rest for long periods of time, which might be a reason for having the green smoothie at breakfast instead of lunch.


Kristin March 13, 2014 at 1:52 pm

Thank you for a wonderful summary on the book and the cleanse. Are you supposed to continue the supplements during phase 2 as well or take them only for the 21 days during phase 1? Thanks again!


Penny Hammond March 16, 2014 at 10:39 pm

I’m glad you find this helpful. Unfortunately I only concentrate on the food side of diets, not supplements…


Maria March 16, 2014 at 3:26 pm

My boyfriend and I are going to start this diet soon! We cannot afford $800 for the supplements/program…there is a health food store in town…would it be all right if we bought the supplements locally?


Penny Hammond March 17, 2014 at 8:05 pm

I concentrate on the food side of diets, and don’t really look into the supplements. Try reading the recommendations in the book and finding something that matches them closely enough.
Good luck with the diet!


Kristin April 28, 2014 at 2:01 pm

Hi Maria,
Yes, that should be fine as long as you find supplements with the correct dosage as outlined in the book. That’s what I did (I got all of my supplements from The Vitamin Shoppe) and only spent ~$130 total on them. Goldenseal is a good choice for the herbal supplement that you’re supposed to take twice a day. Good luck!


cindy smith March 22, 2014 at 2:09 pm

I am on the third week of the program, and SICK of the smoothies. Can hardly get them down. But I am wondering about the tea. Book says herb tea, what is wrong with instant tea?? And WHAT is a green juice?


Penny Hammond March 23, 2014 at 3:27 pm

Instant teas often contain artificial additives and preservatives – you’d have to be careful to find one where the only ingredient is herbal teas.

A green juice is what you get when you juice green vegetables without any fruits or non-leafy vegetables.


JC March 22, 2014 at 2:25 pm

Pls. Is there anything else I can drink or eat in morning besides those shakes? I’ve thrown up every morning and tried everyone. :( Thank you.


Penny Hammond March 23, 2014 at 3:25 pm

Sorry, but the shakes are the only alternative that the author gives for breakfast! As well as the recipes in the book, you could try the ones


M Craig May 15, 2014 at 1:49 pm

If you can’t drink the shakes, how about deconstructing them — can you just eat a cupful of raw spinach and half a cup of blueberries and drink a glass of unsweetened almond milk?


Penny Hammond May 15, 2014 at 8:20 pm

Dr. Junger doesn’t explain in this book why he thinks you should have shakes; there’s some discussion of detox diets in his first book, Clean, where he talks about different types of detoxes which may include shakes. Some discussion points – the fiber is released in shakes and grabs toxins in the intestines so they don’t get reabsorbed; or they’re an easy way to deliver a number of different nutrients. Other diet books talk about giving your system a rest so it doesn’t have to work so hard to digest.

If you really hate the shakes, you could try deconstructing them, making sure you chew really well.


Nieves June 15, 2014 at 1:40 pm

Thank you for a great summary on the Clean Gut Diet Penny, it has clarified a few doubts I had after reading Dr. Junger’s book.

The diet guidelines indicate to go easy on the allowed Legumes (split peas, lentils) as well as quinoa, only a side serving a day. My question is: How much is a side serving of split peas, lentils and/or quinoa?

In addition, would you have any suggestions for green juices?

Thank you again!


Penny Hammond June 19, 2014 at 6:02 am

Glad to help!

I can’t find any guidelines for portion sizes for the allowed legumes and quinoa – Dr. Junger just reminds you to go easy on them. Perhaps about 1/2 cup total maximum per day?

The book asks you to have fresh green juices, which would mean they’re made from scratch. The Healthy Green Drink Diet book by Jason Manheim has a number of green juice recipes – watch out that the ingredients are allowed on this diet, as there are a number of smoothie recipes that have fruits that wouldn’t be allowed.


Lisa Brown July 9, 2014 at 4:21 pm

Looks like a great program, but I am concerned about the protein and fat intake daily.

I cannot digest, red meat, poultry, wild game, anything but fish, for some reason. I eat fish and eggs mostly, daily, but I also have to watch my fish and egg intake as I have very high levels of B12 (just recently checked) so I must watch how much B12 I take in a day. I don’t always eat the yolks in eggs because I am trying to keep the B12 minimized until the level returns to normal, so I eat the egg whites, with the occasional yolk (maybe 4 times a week). I don’t see any other protein sources I can eat. Also, I do not digest fats well. I have to limit fats or my digestion is effected. My current tests say my gallbladder/liver is fine. With these “leaky gut” types of diets, I don’t see, with my limits on fat and the protein sources that I can eat, that I can get enough food, and calories into me daily without starving. Not sure what to do.


Penny Hammond July 10, 2014 at 5:32 pm

Wow, that’s tough. There’s a lot of information out there about low vitamin B12, but not much about what to eat if you have high vitamin B12. The most helpful resource I found was
Has your doctor given you guidelines about how much vitamin B12 you can eat, or just asked you to limit it?
Do you know what the underlying condition is that’s causing the high B12, to look for specific dietary guidelines for that condition? It looks like most people can eat unlimited amounts and it’s flushed out of the system, so maybe it would help to understand what’s causing the high levels.
It could be that, for you right now, more starchy protein sources such as grains and legumes might be a better source of protein and energy. That’s not this diet, you’re correct.
Hope that helps a little bit.


Marisol Brugmann July 26, 2014 at 11:56 am

On page 124 of “Clean Gut” it says ” Higher quality coconut oil will have less coconut taste. Check out
for our favorite brands.” Have not been able to find it at
Would love to know what oils are recommended.
Thank you.


Penny Hammond August 4, 2014 at 6:46 pm

I can’t find anything on or on recommended brands of coconut oil; the only mention I could find was in the Clean Gut blog presale page, where Nutiva coconut oil is mentioned. That doesn’t mean that it’s the only one recommended; apologies for not being able to find any more!


Suvi July 29, 2014 at 1:22 pm

Hi, my husband and I started the program two weeks a go. We followed the instructions strictly the whole time. Now my husband is going fine and he lost 5,5 lbs. How about ME? I gained 2 lbs, felt awful all the time! What on earth did happen and why? Also my stomach swelled and I felt very full 24/7. We both are quite of normal weight but wanted to lose some.


Penny Hammond August 4, 2014 at 7:29 pm

How annoying!
Did you chew your food really well? Sometimes, if you’re not used to eating a particular food, you swallow it as quickly as possible without chewing it and that makes it more difficult to digest, which can lead to bloating.
Also, was there anything you snacked on or ate a lot of?


Sunny August 9, 2014 at 11:31 am

I read the book in Korean verision and then have just started the program.
In the Korean book, there is a saying that strawberry kiss smoothie(from smoothie king) can be substitute for cleangut shake.
I am wondering that there is natural fruitsugar in the smoothie. Is it possible to drink ?


Penny Hammond August 10, 2014 at 8:42 am

A couple of the shakes in the US version of the book contain small amounts of blueberries, which are a low-sugar fruit – and also a number of other ingredients, including dark leafy greens and nuts/seeds. Strawberries are generally considered to be a low-sugar fruit – if the smoothie you’re talking about has only a small amount of strawberries and contains lots of dark leafy greens and some nuts/seeds, it might be okay on this diet.


Georgina August 14, 2014 at 1:31 pm

Gosh! I can tell I will find this difficult to stick to! But I totally want to give it a go! Even if I only start eating 40% better i’ll be so so happy with the results! Thanks for the extensive information.


Jenny September 17, 2014 at 5:33 pm

I was wondering if you could help me with something im a little confused about.. I once read you shouldnt pair 2 proteins, competing proteins.. I often have quinoa and veggies for lunch but i sometimes add pumpkin protein powder for some added protein.. Do you think this is a bad combo? I see you consider quinoa a vegetable protein.. Do you think pumpkin protein powder is also a vegetable protein? Which would make it ok? I hope so because its one of my favorite lunches! :) but i recently am concerned with food pairings for better absorbtion and nutrition.. Thank you for your help!


Penny Hammond September 17, 2014 at 6:37 pm

Dr. Junger says that you shouldn’t pair animal protein and vegetable protein in the same meal – he doesn’t say anything about combining different animal proteins or different vegetable proteins (and I don’t think I’ve heard of combining proteins being a issue with any other combining diets I’ve read about).
Quinoa is a vegetable, and pumpkins are a vegetable, so the proteins in them are both vegetable proteins – it shouldn’t be a problem to combine them on this diet. However, it may be even better to have pumpkin seeds instead of pumpkin protein powder – they’re an unprocessed, whole food (pumpkin protein powder is processed from pumpkin seeds, which are the part of the pumpkin that contains the most protein).


Mi Mi October 13, 2014 at 7:30 am

Hi .I’d like to start the program but I’m not interested in losing any weight. Your thoughts please?


Penny Hammond October 13, 2014 at 9:55 am

The book isn’t about losing weight, although losing weight might be a by-product of the process. It’s about eliminating the root causes of disease – the author says that the root of almost all chronic diseases starts in your gut.

So you can follow the program even if you don’t have any weight to lose.


Jamie Berndt October 26, 2014 at 3:49 pm

Are we able to snack on this plan? On veggies or berries? I don’t see snacks mentioned in the book, but I also do not see them expressly prohibited.


Penny Hammond October 30, 2014 at 9:51 am

The books says you can “have a clean snack” (p.143).
Veggies and berries should be fine.


Jo December 14, 2014 at 9:19 am

Can you direct me to any groups of people or natropathic doctors who can walk me through this. I want to do it with someone. I live in Montpelier VT.




Penny Hammond December 14, 2014 at 2:56 pm

The Clean Program has coaches – see and click on “Talk to a coach”. “We offer Wellness Coach Support as a free service to provide you with personal support before, during, and after your cleanse.”


Ruth December 19, 2014 at 2:10 pm

Yacon or Lakanto?

I thought yacon was one of the allowed sweeteners when I did Clean Gut last January, but now I am seeing Lakanto as one of the three and no mention of yacon. Is yacon ok?

Thank you!



Penny Hammond December 26, 2014 at 1:21 pm

Hi Ruth,
Yacon is listed in the original Clean book, and in this list of sweeteners that are okay to eat in small amounts:
However, it isn’t listed in the Clean Gut book, which was written later. Not sure if that’s because Dr. Junger decided it’s not as good for you, or he was promoting other sweeteners, or it just got left off by mistake.


Muris December 20, 2014 at 7:27 pm

Hi, i have been following this kind of diet for couple of months now but now seem to have developed some kind of severe histamine intolorence that i cannot have meat unless very fresh without causing problems. What would you base your meals around and to get some protein? Ive been mainly having vegtable stews with rice protein shakes and nuts as snacks as well as green juicing, however now im finding nuts and grains are irritating the gut also :(


Penny Hammond December 26, 2014 at 1:44 pm

It sounds like you have an unusual case. You could try reaching out the the Clean wellness coaches – see


Sunny December 23, 2014 at 11:22 am

I did the clean gut program last August. It was great for me! However, I couldn’t endure my stress during Nov~early Dec, I had a lot of snacks for reducing my stress.. So I’d like to try this program again. Is it okay? I mean it would be no problem with my guy if I do it 2 times a year. Should I take all the supplements again?


Penny Hammond December 26, 2014 at 1:56 pm

Hi Sunny!
Sorry to hear you were so stressed for the past couple of months.
How far through the program did you get – did you do any phase 2 reintroduction of foods to see how your body reacts to them? How do you feel in general now – do you think you’d benefit from going through the cleanse again, or would you feel comfortable moving straight to the lifetime diet?
If you already tested foods and saw they were okay, and you want to do the cleanse again, you could probably add the tested foods to the phase 1 foods.
I concentrate on foods, not supplements – if you feel that it’s worth doing the full cleanse again, maybe the supplements would benefit you.


Marisol B December 29, 2014 at 12:30 pm


I’m about to start the program! I already bought the supplements, but I was wondering which other brands of protein powder did you use instead of the Clean Shake? Thanks!


Penny Hammond December 31, 2014 at 1:37 pm

Dr. Junger suggests a plant-based protein, but he doesn’t give alternate brands (of course he’s trying to sell his own brand).
You could try checking in to the online community (registration required) –


Cathy January 4, 2015 at 2:50 pm

Hello and Happy New Years!
Well it has begun. The quest for a healthier me. I am a sufferer of autoimmune disease. I have chronic uticaria and angioedema. I also have been having issues with random stomach issues (getting sick). So. I am done. I am only 47 years old and am shattered that I have become like an old lady internally. I have heard from many sources that trying a clean diet might be the way to go for me. This of course has not been a suggestion from my physician. He sadly scoffs at such healing ideas. I purchased the Clean Gut diet book. I am very excited to try it. Any suggestions?


Penny Hammond January 4, 2015 at 2:59 pm

Happy New Year to you too!
I suggest you keep a food and symptom diary to see how you’re doing. At the beginning you may have some worse symptoms, especially if you’re used to eating a lot of processed foods, sugar, or caffeine. But after detox symptoms go away you may start to feel better, although it might not happen straight away. Good luck.


sarah January 8, 2015 at 3:00 am

Hi Penny- are fresh prawns allowed? Also, store bought almond milk- what ingredients are allowed? I’m having terrible trouble finding clean approved almond milk. Thanks very much! Sarah


Penny Hammond January 10, 2015 at 12:36 pm

Hi Sarah,

Whenever Dr. Junger mentions seafood, he talks about fish but not shellfish. He doesn’t say to avoid shellfish… but they’re often contaminated so that might be why he doesn’t list them as okay to eat.

Have you ever thought about making your own almond milk? Search the internet for “almond milk recipe” or whichever one you want to make.
Generally, you grind the nut and add to water and blend well, or put nuts and water in a blender and blend well, then strain the mixture.


sarah January 12, 2015 at 12:10 am

Thanks very much Penny- this page has been very helpful! :)


Lisa Brown January 12, 2015 at 9:38 am

Hi, there.

The cleanse calls for an herbal anti-microbial and I saw the one recommended, Tricycline which is over $40. Is there a less expensive option out there? I have been looking around and can’t find many of this type of supplement, a blend. Can one just take Berberine? Thank you and happy new year :)


Penny Hammond January 12, 2015 at 8:17 pm

Hi Lisa, and happy new year to you too!
I look at the food side of diets, and I don’t know about the supplements. Can anybody else help?
You could try checking in with the coaches (they say this is a free service) –


Christina January 27, 2015 at 3:13 pm

Question: The book calls for using coconut milk, but it doesn’t say what kind. The canned variety or the kind in the carton? If it’s interchangeable with almond milk, I’m assuming it’s the kind in the carton, but it’s not clear.


Penny Hammond January 27, 2015 at 4:03 pm

Dr. Junger says “You can use canned coconut milk, but it’s very rich and some brands may have additives. Read the ingredients and, when in doubt, make your own. You can also use coconut milk in a carton from the health-food or grocery store. Make sure it’s unsweetened.” (p.159)


Saul February 10, 2015 at 5:02 pm

OK day 2 so far so good

quick question
in the Clean Gut diet it says no caffeine or caffinated beverages

but it also says you can drink green and white tea (both of which are caffinated)
and yerba Mate ( caffinated)

as a coffee drinker, I’m looking for a milder solution than cold turkey
with this part, can anyone help a brother out?



Penny Hammond February 13, 2015 at 2:27 pm

You’re correct – green tea, white tea, and yerba mate are listed in the “Clean Gut Diet Food List” (p.95)
It could be because these teas tend to have a lower level of caffeine than coffee or regular tea. See the mg/fl.oz. column at CaffeineInformer (click on Coffees or Teas to see the data).
Or it could be because they have other beneficial compounds that offset the caffeine.
Or it could be that when Dr. Junger said “avoid caffeine” he meant “avoid coffee and caffeinated soda.”

Would one of these teas work for you as a substitute for coffee?


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