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

by Penny Hammond on June 24, 2013 · 61 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
  • 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.

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