How To Do An Elimination Diet

by lydia on May 8, 2013

If you are someone that struggles with food sensitivities, constant immune issues, seasonal allergies, skin issues and more, doing an elimination diet would be a good idea. I know this is not necessarily an easy or desirable thing to take on, however, it’s really one of the most effective ways to get to the root of your issues. Remember as Hippocrates once said; ‘All disease begins in the gut’. It’s a good first step for anyone to take in trying to further iron out ongoing  health issues.

Basically an elimination diet is a 3 week (minimum) to 3 month diet that removes the most allergenic foods (such as- gluten grains, dairy, soy, corn, peanuts; if you know you are intolerant to gluten you’ll need to include all the gluten cross reactive foods in your elimination plan). The goal is to remove any foods creating an allergic/immune response in the body and heal the gut. When you’ve completed the allotted time you can start to add foods, one by one, back into your diet to see which may provoke symptoms. You might want to keep dairy and eggs out of your diet for up to 3 months,  and gluten containing grains for 6-8 months to get the best results on those particular foods. You’ll need to become a label detective and know all the hidden sources of gluten, dairy and eggs. You can also exclude any foods you may believe to be suspect. Everyone will be different.


There are a few protocols out there that I am familiar with that are excellent – SCD (the Specific Carbohydrate Diet) and GAPS (Gut and Psychology Syndrome) are lifestyle protocols to heal and repair the gut but are not short term by any means. Most who go on these are on them for a long time working to heal and repair the villi in the gut. The introduction diet for the GAPS plan is essentially an elimination diet, though it does not exclude dairy. Pick up a copy of the book and follow the instructions on how to do the introduction part of the diet. Keep in mind it may take some time – plan on at least one month or longer. I also like the Whole 30 plan as an elimination diet. The Paleo Autoimmune protocol is even more in depth, and I would recommend working towards that if you have a known autoimmune condition. Once an autoimmune condition sets in, healing the gut should be the top priority to help stop the attack on the bodies tissues/organs and prevent other autoimmune conditions from setting in.

Elimination Diet Game Plan

  • My personal recommendation would be to start out on a Paleo diet for 3 months. I like something like the Whole 30 challenge because this removes most of the gluten cross reactive foods as well. This plan should get you good results.  This removes the big common allergens, like dairy, grains, legumes and even sugars. Or you could do a GAPS approach removing the dairy as well -remember casein is becoming more of a  problem – you do want to rule that out. The GAPS approach allows honey, which might be more doable for some, though make sure you don’t eat more than 2 Tbsp of honey per day. Just because it’s allowed doesn’t mean the sky is the limit.
  • After 3 months if you still find you have some symptoms go ahead and remove eggs for 3 months. After another 3 months you may feel great or still have some minor symptoms. If you feel good and have seen your skin issues etc… clear up, you could try to reintroduce some dairy or even try duck eggs. If you still have some symptoms sticking around try removing nuts and any gluten cross reactive foods (see list here), then after that try nightshades. Keep in mind, finding all the problematic foods may take some time. This is not a formula that you can expect exact magical results, this is a game plan to help guide you on a journey of self-exploration as to what your body can and cannot handle at this time. If you don’t want to self explore, you can get blood work (see below) to help you at least have a good starting point.
  • If you really want to cut to the chase and know for sure what foods you need to remove – I recommend asking your doctor/health care practitioner to order Cyrex Labs Array #4. If you cannot get your doctor or a practitioner to order this test for you – you can order it yourself through True Health Labs for $269. (click image further down in the post)
  • While you are doing an elimination diet it will be critical to work on healing the gut through supplementation and certain healing foods (many of which are included in the GAPS protocol).
  • Planning will be key. Once you decide to take on an elimination diet, you will need to plan well if you want to succeed. Plan to start during a time where life is not quite as stressful. One thing you can do is start by having one meal per day that fits your new diet plan. Do that for 1-2 weeks, then add another meal for 1-2 weeks, then add another. Then add snacks if needed. Then figure out the foods you can eat outside of the home and get a game plan for how you will handle that. Include in your game plan what portable foods you can take with you when you are out so you don’t find yourself straying from your plan while you are out.
  • While you are gearing towards the complete elimination diet plan, try to set some food aside as you can. For example, if you can double a dinner recipe do it – you’ll be so glad you did. Also, have planned leftovers and learn to shop in bulk and keep a stocked pantry. One of the biggest trip ups people run into on an elimination diet is when life gets busy and you haven’t been as prepared as you would like. The more time you take gearing up the better of a success you may have sticking to the plan for a longer duration and really giving your body a chance to heal/recover.  If you decide to jump in all at once to an elimination diet, then realize the first 3-4 days or even week will be the hardest. If you go with something like the Whole 30 Plan -they have resources available to help you get started, such as foods, even meals you can order online and recipe books.
  • Keep meals simple. You don’t have to be a rockstar in the kitchen. Meats and veggies make easy meals and very satisfying ones with some fruit for dessert. Vary what you eat to avoid issues developing more sensitivities. Eat regular meals the same time every day – you want to keep your blood sugar stable and your circadian rhythm happy too. Eat lots of varied fresh, in- season, low glycemic veggies.
  • Don’t replace sweets with yet more sweets just in the ‘allowed’ form. This is one thing that drives me nuts – when I see people baking gobs of GAPS or Paleo treats, just because they are made with ingredients from the ‘allowed’ foods list. Listen, eating baked goods daily with almond flour still is not a great idea even if nuts are allowed. Use those baked goods as the occasional treat, not a staple of your diet.

If you want to learn more about digestion overall and how to repair & restore your gut health, please click the image below to find out about my next run of my ‘Heal Your Gut‘ online course!

Revitalize Your Health is a comprehensive step by step online course to help you get your health where you want it to be. I cover metabolic health, sleep, fitness, diet, hormonal health, how to gently detox the body, the home and even how to raise healthy kids. Improve your cardiovascular health and keep it in shape all year. Plus. learn how to implement other healing practices into your life to balance out diet and exercise. It’s all here for you – come on over and find your best health this spring! Revitalize Your Health – What It’s All About!


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Debra E May 10, 2013 at 12:11 pm

Excellent information Lydia! Which, if any, have you done? I appreciate your comments about the sweets. I started the GAPS intro last week and didn’t realize the extent to which food is tied to my mood and emotions. I’ve been looking forward to getting off intro and being able to make an allowed sweet that I can have in the evenings. I can see, after looking through the Paleo Auto-Immune protocol that perhaps it would be best for me to not include ANY of that for even longer :( Though sad, it’s very helpful. I’ve been wanting my husband to agree to let our 6yo diabetic daughter (and thus all of us) go on the GAPS diet so that is part of the reason for me going through it (plus I want to heal my depression). I’m testing it out so he can see if it “works” and then go from there. But after reading the Paleo Auto-Immune protocol I am wondering if perhaps that would be even better for her? Any thoughts on this?

lydia May 10, 2013 at 2:55 pm

I’ll be honest and say YES! I think the auto-immune protocol could be worked up to though and starting with GAPS is a great segeway!

I’m actually working my way towards the autoimmune protocol but will be getting some testing done first to find out if I”ve missed any hidden food sensitivities. I’ve done the Whole 30 a few times and love it -it’s annual clean up for me. I’ve done GAPS in small spurts and have done the Intro diet as well.

Chris Musser May 11, 2013 at 12:39 am

Lydia, this is a spectacular guide! I’ve been on an elimination journey for three years now. I agree that taking things in steps is the most sustainable way to go, especially for those with the brain fog, fatigue, pain, disability, and stress that go hand-in-hand with chronic health conditions.

Five years ago, a naturopath looked at me, disheveled, depressed, and obese, and a diagnosis of “mildly hypothyroid,” with my two spirited young children in tow, and told me she thought I was “too overwhelmed” to go gluten-free/casein-free.

Two years later, I self-diagnosed myself with Hashimoto’s and gave up gluten for six months gave me enough stamina and mental clarity that I could go on GAPS. Made more progress, but made the mistake of too many almond flour apple cinna-muffins. :-) My daughter was diagnosed with epilepsy and we all went on a ketogenic diet–basically low carb primal (ghee, cream, yogurt and aged cheeses were still in our diet) eliminated my blood sugar issues and I started losing weight without ever feeling hungry. (And our daughter’s seizures are well controlled with her diet.) Giving up nightshades made a big difference for my skin, but I’m going to cut out eggs and dairy for a bit and see if that makes a difference.

Along with supplementation, I found chiropractic care, massage, physical therapy, and talk therapy invaluable. I call it “Taking Care of Chris-ness”

I have gone from being too tired and in too much pain to get off the couch to launching a personal chef service for people following special diets. I’m on my feet 8-10 ours a day and feel better than I have over a decade.

Debra E May 16, 2013 at 9:37 am

How do you really know what you should do? How does one unpackage all this stuff? I am currently doing the GAPS intro but then am not introducing dairy ferments or nuts or eggs or nightshades after looking at the auto-immune protocol. I don’t have an auto-immune disorder (unless allergies are considered that) but there is a strong family history of it with a diabetic daughter and a mother, her brother, and their deceased father with RA. I really don’t want to go through this all again so I’m just combining GAPS intro with Paleo Auto-immune protocol. But then I hear of oxalates, MTHFR (whatever that is), and high FODMAP fruits and veggies. Is there a test for all this stuff to know what I should really avoid or not? It’s making my head spin trying to get it just right!
On a side note, after waiting 3 months for my sauerkraut to get done and hearing how delish it is, I found it to be just OK but not spectacular. Since introducing it on the GAPS intro it’s amazing how delish it tastes now! It’s my favorite food. It feels like my dessert! How funny things are when you eliminate.

lydia May 18, 2013 at 8:53 am

First of all – you need to take a DEEP BREATH…………….maybe another one?!!

Okay, so if you try to figure out every single thing today you’ll go crazy and then you will never start anywhere. Starting with GAPS intro is GREAT!!!!!! I’ll be honest and say -don’t worry about all that stuff right now (yes there are tests for oxalates, food allergy tests could be good, and tests for MTHFR which I do not know how to decipher as of yet, but you can go to and order the testing for just $99). However, I recommend just focus on the process of the GAPS intro -this is a very powerful protocol and you don’t want to rush it. If you are on intro for 3 months or more, it may be time to do some other detective work – but I recommend you work with someone to relieve the stress about figuring it all out on your own. If you are a big stress ball about it all you will hinder your own healing – support is good. I highly recommend letting some of it all go until you feel peace about exploring it further or find that you need further help than just what intro provides. Does that make sense?

So glad you are loving your kraut -it’s amazing stuff. I am running my next Heal Your Gut course July 10th and am also running an elimination diet challenge for the summer! You may want to check one of those options out…….

Debra E May 20, 2013 at 11:35 am

Thank you Lydia for helping sort it all out! I don’t have any kind of support but see how it would be beneficial. I think there is a GAPS group on Yahoo? I will continue to leave out eggs, dairy, and nuts for the moment as I go through GAPS intro but forget about the rest for now. Thank you for the heads up on your upcoming class. I missed it last time as I was doing your “Get Healthy to Lose Weight” course. Can you answer a couple more questions? If avocado feels tingly and perhaps itchy in my mouth and itchy & uncomfortable on a place in my back shoulder, does this mean I might be sensitive? It did this as well even when I wasn’t on GAPS. All other foods seem to be going well. Thanks!

lydia May 20, 2013 at 1:43 pm

You’re welcome!

It sounds like the avocado is giving your body some allergic tension. I’d remove it for awhile and maybe try again down the road after you’ve healed a bit.

Tina March 1, 2015 at 1:50 pm

Lydia, Wondering if you could offer your thoughts. My family and I are on the GAPS diet. My 1 year old also went on the Intro diet with us when we did it. He has always done great and never showed any reaction to any foods. However, several weeks ago I got too excited about him enjoying raw duck yolks, and I think gave him too much too fast over just a couple of days. His cheeks got really red and looked liked eczema had settled in. I immediately took the yolks out of his diet and put him on GAPS intro. However, after 2-3 weeks on GAPS intro first stages, he is still having an eczema flare up all over his cheeks and chin when he eats, even just with boiled meats and veggies! Not sure what I should do from here…any thoughts?

lydia March 18, 2015 at 4:11 pm

Do you have a GAPS practitioner you are working with?

I don’t work with that diet in specific – I work more with folks to correct the underlying biochemistry. Some kids have eczema issues related to heavy metals and copper and need to eat differently because of oxidation rate vs. a specific diet. That said, it sounds like he is having a reaction to something whether it’s a food or stress related.

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