Achiness and Gut Issues 30 Days into Paleo?

Here’s a question from a reader you may be able to relate with. My answer is below.

Neely,Like so many others I appreciate your web site, and your generosity in replying to these questions.

I am 60, have a hypothyroid, and continue to suffer from hot flashes to the point where I take a low dose of bio-identical hrt to manage this. And in retrospect was suffering many s/s of overall inflammation.: joint pains, fatigue, weird skin things, brain fog, a feeling of being toxic, almost impossible to lose weight, and an ‘uncomfortableness’ after having a BM. I had loose stools, and discomfort after defecating.

In the Fall I started going towards a Paleo lifestyle. At first gradually (80/20). Like so many others I was amazed. I felt better than I had in years, dropped a few pounds, skin was clearer, and my bowels straightened out. Great! By the time I started on the 30 day challenge I was already 95%. Paleo. What I gave up primarily was my cream for the one cup of tea I had in the AM., and occasionally cheese.

Things went well, until the 4th week. For the past 5-6 days, my gut has been much inflamed. Over the past days I have not been feeling well. I am achy all over, tired, and my bowel picture seems to have reverted to the pre dietary change mode, but worse.

So my question is could this be a delayed detox picture? I really did not have any negative symptoms at the beginning.

My diet has been fairly consistent during the Whole 30. Breakfast is usually eggs, with veg, or sausage and a sautéed apple in coconut oil. Sometimes 1/2 of a sweet potato, or some winter squash. Lunch: a large salad with chicken or tuna with homemade mayo, or olive oil and lemon. I have almonds for snacks or sunflower seeds. Dinner is meat, fish, or chicken and I get organic when feasible, with green veg, and paleo okay carbs such as squash, plantain etc. I eat 2 pieces of fruit a day.

In the past few days I have eliminated raw veg, and mostly eating chicken and winter squash. Today is the second day I am lying low.

I am confused, today is my 30th day. Any input would be very welcomed.


Well, it sounds like you’re doing all the right things, and I’m really happy to hear you were having so much success! It’s unfortunate you’re having problems now, but I’m confident you can figure out this issue.

It’s a constant process weeding out the things that make us feel bad and adding more things in that make us feel good, so just stick with it and you’ll get it eventually!

It’s hard to say what’s going on, but these are the things that come to mind:

1) Maybe you’re not getting enough probiotics in your diet. I’d go get like a 50 billion organism probiotic supplement from the health food store and take it once a day. Or get Inner Eco from a health food store (fermented coconut water). And/or eat more cultured foods like raw sauerkraut, kim chi, etc.

2) Could be you’re getting something you’re sensitive to in your diet you’re not aware of? Have you changed anything, even started taking a supplement in the last week that has weird ingredients, or a pharmaceutical change?

3) You could be sick. Like, as in, a stomach bug.

4) You could be responding to one of the foods you’re eating all the time. My first inclination is the nuts and seeds. They give so many people problems that I’d experiment with those first if you think it could be contributing.

But a detox 4 weeks after starting Paleo? I’ve never heard of that, so I think it’s probably something else. I wrote another blog post on the reasons people get gastrointestinal stuff while on Paleo, called “Still Having Digestive Problems While Eating Paleo” that you should read. There are more ideas in there about what to try and why this is happening.

In any case, I wish you all the best in figuring this out!

What have you, dear readers, found was the culprit when you had digestive stuff after going Paleo?


  1. Perhaps the gut has not had a chance to heal, and/or there is an ongoing food intolerance, as you are saying. I agree with the probiotic suggestion. Also, a digestive stool analysis, which would reveal a gut pathogen or an elimination diet would help get to the root cause of the intolerance. Then there is also food sensitivity testing, IgG food antibodies.

    Garlic has antibacterial properties, and although we are not sure what pathogen or yeast we are dealing with, natural anti fungals include the caprylic acid in red palm oil.

    At some point, you may consider professional help because without that type of evaluation you may not know if the “toxic” reaction is a pathogen, or if your fatigue is a result of micronutrient deficiency or toxic substance overload.

    I would like to encourage you to stick with the healthy changes you are making. It could be that you are bringing toxic substances out of storage/hiding in a compartment like fat. That could affect mitochondria adversely.

    You might consider a Paleo friendly fruit smoothie with organic greens like kale, parsley, spinach or cilantro (rotate daily) as they are packed with the micronutrients you may be in need of right now. They will help feed the good probiotics, and you can possibly spike your smoothie with a gut healing anti-inflammatory product that can boost up your ability to detoxify and help heal your gut lining as well.

  2. First off, I totally understand, I have been dealing with severe thyroid/autoimmune disorders for years, and the only thing that makes me feel better is eating paleo with some exercise and yoga. Well, I agree with probiotics helping BUT I know tuna is something that should rarely be eaten by people with thyroid or autoimmune issues because of the mercury. Also, glutamine supplement helps the tummy feel better.

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