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21 Day Comprehensive Elimination Diet

GI FIX Gut Restore Protocol through Functional Medicine

Welcome to the REMOVE step of the 5 R's of Functional Medicine (REMOVE, Reinocculate, Replace, Restore, Rebalance). The 21 Day Comprehensive Elimination Diet, designed to clear the body of harmful foods and chemicals you may be allergic or sensitive to, improve gut function, and reduce the inflammatory burden.

The supplements within G.I. FIX completes the last 4 steps of the 5 R's. These clinical grade supplements are designed to work optimally in conjuction with the Elimination Diet and can provide powerful benefits to those with any level of intestinal distress, depression, fatigue, anxiety, headaches, fibromyalgia, or other chronic ailments.

The purpose of this dietary program is to allow your body’s detoxification machinery, which may be overburdened or compromised, to recover and begin to function efficiently again. These dietary changes help the body eliminate or “clear” various toxins that may have accumulated due to environmental exposure, foods, beverages, drugs, alcohol, or tobacco use. This program also helps to significantly reduce inflammation throughout the body, thus promoting healing and optimal functioning for the other bodily systems as well.

This is called an “Elimination Diet” because you remove certain foods and food categories from your diet which have proven to be the most common culprits for many gastrointestinal symptoms and conditions. Upon completion of the three week elimination period, you’ll begin systematically adding foods back into your diet one at a time to determine which foods may be triggering symptoms.

Functional Medicine Diet BendWhile undergoing the 3 week elimination period, it is important to eat a wide variety of foods and do not try to restrict your calorie intake. In addition, it is vital to read all food labels carefully and avoid any foods in which the ingredients seem unclear. If you find no improvement within three weeks it is safe to assume that: either you don't react to the foods that have been removed (meaning no food allergies), or you may have food allergies but there is yet another factor causing the symptoms to continue. There are no magical answers here; this is a journey of self-exploration and discovery. While this process may seem daunting at first, most will experience significant relief from a variety of symptoms and will find this process extremely beneficial in pinpointing specific food triggers. In fact, most doctors who prescribe the elimination diet to patients find it to be one of the best clinical tools available for getting to the root of many dietary sensitivities and irritants.

While there really is no "normal” response to this diet, most report increased energy, mental alertness, decreased muscle or joint pain, and a general sense of improved well-being. However, some will experience initial reactions to the diet, especially in the first week, as their bodies adjust to a different dietary program. These symptoms may include: changes in sleep patterns, lightheadedness, headaches, joint or muscle stiffness and changes in gastrointestinal function. Such symptoms rarely last for more than a few days. A person’s initial response to any new diet is highly variable and the elimination diet is no exception. These differences can be attributed to physiological, mental, and biochemical differences among individuals as well as the degree of exposure to, and type of “toxins” being eliminated and other specific lifestyle factors.

Following the Plan:

If you haven't already, please click here to access a list of the foods that will be allowed during the 21 day elimination phase. These Guidelines are intended as a quick overview of the dietary plan. Eat only the foods listed under “Foods to Include”, and avoid those foods shown under the “Foods to Exclude” category. When shopping and selecting foods read labels closely and opt for those foods with the fewest ingredients and least amount of processing. The majority of foods consumed during the 3 week period should be fresh and in whole, unprocessed form. If you have a question about a particular food, check to see where it is located on the food list. It is advised to use the rule of "when in doubt, leave it out" on this plan. In addition, you should, of course, avoid any listed foods to which you know you are intolerant or allergic. Specific changes should be made to these guidelines based upon recent food allergy/sensitivity testing and personal health conditions and history.


  • The first 2-3 days tend to be the most difficult. You can make this transition easier by becoming familiar with the foods allowed and stocking up on them ahead of time to ensure easy and convenient access to these foods.
  • Plan your meals ahead of time or create a weekly menu to make planning easier.
  • Eat simply. Cook simply: Make a pot of chicken-vegetable-rice soup, make a large salad, create a stir fry with a variety of vegetables topped with fish or chicken, or simply grill a serving of meat or fish and enjoy with a side of vegetables.
  • It may be helpful to cook extra chicken, sweet potatoes, rice, and beans, etc. that can be reheated for snacking or added to another meal. Use these leftovers for upcoming meals or snacks, e.g., leftover broiled salmon and broccoli from dinner as part of a large salad for lunch the next day.
  • Have prepared food on hand so you can grab something quickly when necessary (vegetable sticks and fresh fruit)
  • Eat frequent (every 2-3 hours) and balanced meals (try to include a protein, fat and fruit/vegetable with most meals). This will keep blood sugar levels stable while preventing you from getting too hungry and being tempted to stray from the plan.
  • Avoid any foods that you know or believe you may be sensitive to, even if they are on the “allowed” list.
  • Try to eat at least three servings of fresh vegetables each day. Choose at least one serving of dark green or orange vegetables (carrot, broccoli, winter squash) and one raw vegetable each day and vary your selections as much as possible.
  • Buy organic produce when possible and select fresh foods whenever you can. Wash fruits and vegetables thoroughly. Click here for a list of recommendations for foods that should always be purchased in organic form.
  • If you are a vegetarian, opt for larger amounts of protein-rich legumes as well as rice, quinoa, amaranth, teff, millet, and buckwheat.
  • If you are consuming coffee or other caffeine containing beverages on a regular basis, it is advised to slowly reduce caffeine intake prior to beginning the elimination diet rather than abruptly stop it to prevent caffeine-withdrawal headaches. For instance, try drinking half decaf/half regular coffee for a few days, then slowly reduce the total amount of coffee. Decaffeinated herbal teas make a wonderful replacement for coffee.
  • Read oil labels and use only those that are obtained by a “cold pressed” method.
  • When selecting animal sources of protein, look for free-range or organically raised chicken, turkey, or lamb. Prepare by baking, stewing, grilling, or stir-frying. Cold-water fish (e.g., salmon, mackerel, and halibut) is another excellent source of protein as well as omega-3 essential fatty acids, which are important nutrients in this diet.
  • Remember to drink the recommended amount (at least two quarts) of plain, filtered water each day.
  • Strenuous or prolonged exercise may be reduced during some or the entire program to allow the body to heal more effectively without the additional burden imposed by exercise. Adequate rest and stress reduction is also important to the success of this program.
  • This is NOT a weight loss program. If you need to lose or gain weight please Contact Us for specific recommendations and guidance.

POSSIBLE PROBLEMS: Most people feel consistently better each day during the elimination diet. However, if you are used to using caffeine, you may get withdrawal symptoms the first few days which may include: headaches, fatigue, irritability, malaise, or increased hunger. If you find your energy lagging, you may need to eat more frequently to keep your blood sugar and energy levels stable. Be sure to drink plenty of water.

Gut restoration program 5 Rs of functional medicine

After the 21 Day Elimination Period

TESTING INDIVIDUAL FOODS: Once you have completed the 21 day elimination period you can begin to add foods back into your diet. Be aware that the process of transitioning off of the elimination diet is even more important than the process of eliminating foods, especially for those who notice drastic improvements in symptoms as process of reintroducing foods should allow you to pinpoint exactly which foods are causing symptoms.

It is very important to KEEP A JOURNAL OF ALL FOODS EATEN AND ALL SYMPTOMS. Be sure to add foods one at a time, one every two days. Eat the test food at least twice a day and in a fairly large amount. Often an offending food will provoke symptoms quickly—within in 10 minutes to 12 hours. Signs to look for include: headache, itching, bloating, nausea, dizziness, fatigue, diarrhea, indigestion, anal itching, sleepy 30 minutes after a meal, flushing, and/or rapid heartbeat. If you are unsure, take the food back out of your diet for at least one week and try it again. Be sure to test foods in a pure form: for example test milk or cheese or wheat (one at a time), but not macaroni and cheese that contains milk, cheese and wheat! When adding in nuts it is recommend to add in one variety of nut at a time. For instance add almonds then wait a couple of days and add walnuts; as opposed to adding all varieties back in one day.

THE RESULTS: By avoiding symptom-provoking foods and taking supportive supplements to restore gut integrity, most food sensitivities will resolve within 4-6 months. This means that in most cases you will then be able to again eat foods that formerly bothered you. In some cases, you will find that the irritant or sensitivity doesn’t go away. In this case either you must wait longer or it may be a “fixed” allergy that will remain lifelong.

AFTER THE TESTING: It would be advisable to return to your health practitioner for a follow-up visit to determine your next steps. If you find allergies to many foods, you may want to explore a 4-day food rotation diet. Finally, anytime you change your diet significantly, you may experience such symptoms as fatigue, headache, or muscle aches for a few days. Your body needs time as it is "withdrawing" from the foods you eat on a daily basis.Your body may crave some foods it is used to consuming. Be Patient! Those symptoms generally don’t last long, and most people feel much better over the next couple of weeks.

Changing food habits can be a complex, difficult and sometimes confusing process. It is important to realize and remember that this doesn't have to be a difficult process! Please feel free to browse our various recipes and other information to make these dietary changes as simple as possible. In addition, if you have any questions about the diet, or any problems, please Contact Us to speak with our Nutritionist.

For a complete list of foods to eat and foods to avoid- Click Here

(c) 2012 The Institute for Functional Medicine. Used with permission granted by The Institute for Functional Medicine, No part of this content may be reproduced or transmitted in any form or by any means without the express written consent of The Institute for Functional Medicine, except as permitted by applicable law.