So You’ve Been Diagnosed with an Autoimmune Disease – Now What?

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Seasoned travellers on the autoimmune wellness journey, this post is not for you. Well – who is it for, you ask? Anyone in your circle who you’ve heard has received an autoimmune diagnosis, send them here! This is meant to be a gentle, encouraging introduction to the topics we talk about here at Autoimmune Paleo.

First steps

Having just received an autoimmune diagnosis, the first thing you need to know is that yes, there are things you can do to live well, despite autoimmune disease. When I was diagnosed with my autoimmune diseases I remember feeling hopeless, confused, and powerless. It took me awhile to realize that I was not destined to a life full of misery and illness. In fact, I started this website in an effort to share research and information about how those of us with autoimmune disease can live healthier, fuller lives (if you need some inspiration — check out the Stories of Recovery!).

Initially, you may be skeptical of any “natural” approach to healing — after all, if it worked, wouldn’t the medical community be more supportive? While conventional medicine is just starting to come around to effective methods of managing autoimmune disease that don’t involve drugs or surgery, literally thousands of people, with all sorts of conditions have found the path to better wellness by dialing in factors completely within their control — like diet, sleep, stress management, and support. Sometimes people are successful with a completely natural approach, others need a combination of conventional and natural approaches. Every one of us, even those that share conditions, are on our own journey to find out what is going to produce the most impact.

It is important to note that I’m not suggesting giving up on your doctor and seeking healing through diet and lifestyle. What I am suggesting is using the best of both conventional and natural medicine, as well as doing everything in your power to live your healthiest life. This includes learning how to best advocate for yourself in your doctor’s office, along with finding out which dietary and lifestyle modifications are best supportive of health. This approach is not only smart (I mean who wouldn’t want to do everything they can to be successful?), but also places the responsibility of guiding this process with the patient (that’s you!).

Embarking on a journey to autoimmune healing can be long and complex — and you have probably noticed all of the information there is out there. I’ve written this article to introduce you to some of the key areas to focus on early on in your journey, and avoid overwhelm. Take it slow, be gentle on yourself, and settle into the process.

Learn about your disease

Learning more about both autoimmune disease in general as well as your specific condition helps you become a savvy, informed patient that can best advocate for yourself during a healthcare appointment. Since we aren’t ignoring conventional medicine or our doctor’s advice, this piece is incredibly important, as it helps you to be proactive and guide the medical side of treating your autoimmune disease.

If you haven’t already, take these steps, in order, over the course of 2-3 weeks:

  • Take some time to read some basic articles on how autoimmune disease works (start with this one and this one). You want to have an understanding of how an autoimmune disease is not a disease of one particular organ, but a malfunctioning of the immune system. This understanding is key to understanding how to live better despite an immune system gone awry.
  • Next, research the basics of your specific autoimmune disease (here are some common ones — Hashimoto’s disease, Crohn’s disease, ulcerative colitis, psoriasis, multiple sclerosis, and lupus). You want to know the key factors about your condition. There are over 100 types of confirmed autoimmune diseases, so there is quite the spectrum of what you can discover here!
  • From there, some more time to thoroughly research your disease and let this information sink in. Start with any support or advocacy organizations and comb their information, perhaps moving to books or other resources aimed towards the layperson (it is important not to get too bogged down with the science, to avoid overwhelm). You know you are on the right track when you can answer the following questions:
    • How does my autoimmune disease affect the body, and which symptoms should I be looking out for?
    • Should I be seen by a specialist or can treatment of this disease be handled by my primary care doctor?
    • Which tests do I need to get on a regular basis to monitor my disease?
    • What are the conventional treatments for my disease?
    • What are the uncommon, or more experimental treatments for my disease?
    • How can I expect my disease to progress over time?
    • Are there any other complications I should be on the lookout for?
    • Is there any ongoing research for my autoimmune disease?

After completing this work, you should have a good working understanding of autoimmune disease as well as your specific disease. You can use this to ask your doctor intelligent questions, as well as help guide and follow your care. It never hurts to be a well-informed patient, and you will start out getting a higher quality of care from your providers.

Learn about what you can do

Many people don’t think that there is anything they can do to live better with autoimmune disease, but that couldn’t be further from the truth! After you’ve learned about the conventional and medical side of your care, you should explore natural and DIY approaches to healing. Be warned, there is a lot of information here, and sometimes it can seem like drinking from a fire hose! Take your time to let this information sink in, and make any changes you decide on slowly. They are the ones most likely to “stick”, and provide lasting impact on your health.

  • Diet: Science has proven a clear link between diet and autoimmune disease, and we believe the Autoimmune Protocol is the best way to find out for yourself which foods are causing an issue. Start here:
    • What is the Autoimmune Protocol and how do you do it? If you are easily overwhelmed, pick up a copy of A Simple Guide to the Paleo Autoimmune Protocol by Eileen Laird. If you’d like to know the in-depth deets about the science and the “whys” behind the protocol, pick up a copy of The Paleo Approach by Sarah Ballantyne PhD. I recommend starting with reading at least one of these books to plan and prepare before embarking on your initial elimination diet.
    • For some free, practical resources for starting the Autoimmune Protocol (like a list of foods to include, avoid, 2-week meal plan, shopping lists, and more resources for beginners), sign up for our newsletter here.
    • The Autoimmune Protocol might be too big a leap for you to make at this time, and that is okay! I recommend that you consider trying a gluten-free diet at the very least (read this article, this article, and this article, for some “why’s”!). You can always consider the Autoimmune Protocol after you’ve made an effort to start transitioning your diet.
  • Lifestyle: Besides diet, there are other areas in your lifestyle you can (and should!) adjust, for maximum healing potential. Check out the following:
    • Sleep — your body won’t be able to regenerate and restore itself if you aren’t getting enough quantity or quality of sleep every night. Need to troubleshoot here? Check out this article, and this article, or the program Go to Bed by Sarah Ballantyne, PhD.
    • Movement — are you getting enough, or even too much exercise? Believe it or not this can have a positive, or negative impact on your autoimmune disease. Read more about my struggles with exercise and autoimmune disease in this article, or more information in this article.
    • Stress management — this is one of the most under-appreciated, yet effective tools at managing autoimmune disease. Many people aren’t familiar with the concept that just having an autoimmune disease causes an incredible amount of stress, not to mention the stressors of our modern life. I recommend reading this article, as well as the book Adrenal Fatigue: The 21st Century Stress Syndrome by James Wilson to learn how to tackle this important piece.
  • Support: In order to make some of the changes outlined above, you are going to need to make sure you have a great support network.
    • Set aside some time to talk to your family and close friends about your autoimmune disease, the measures you are taking to manage and any way they can best support you. This article and this article have some great tips on assembling and strengthening your support network, this article has some fantastic information for your spouse and this article talks about the many faces of support.
    • Seek out connection and community with others who share your diagnosis or who are also doing the Autoimmune Protocol. Check out our list of local meetup groups here or search Facebook for some options.

I’ve only barely scratched the surface of sharing what you can do to help manage your autoimmune disease – remember, this is meant to be a concise, gentle guide! All of the resources I’ve mentioned above should open you up to new areas and avenues of healing to explore. Most of us have been at this process for years, so don’t expect to change everything or fix everything in a day (or even a month!). Information provides the foundation for empowerment, and I’m hoping this guide helps spark some interest in the areas you can explore to boost your health.

Resources that should be on every autoimmune patient’s list

Lucky for you… there is a LOT of information out there about the Autoimmune Protocol, and the natural approach to healing (as opposed to the literal zero resources when I started – consider yourself lucky!). I’ve made a list of the few places to start below, before moving on to deeper topics.

  1. The Paleo Approach by Sarah Ballantyne — This is the book that started the Autoimmune Protocol revolution, and Sarah lays down all of the science and protocol details within. She also tackles the science behind the lifestyle modifications that help those of us with autoimmune disease, like dialing in sleep, stress management, and movement.
  2. The Autoimmune Wellness Handbook by Mickey Trescott (that’s me!) and Angie Alt — This is a co-authored guide to autoimmune healing that approaches not only diet and lifestyle, but other important factors like how to inform yourself, how to best collaborate with health care practitioners, and how to get the support you need on your healing journey. Full of self-assessments, checklists, tools, and other resources, it is a great guide to the healing journey! You can also check out the free, complimentary podcast series here.
  3. The Phoenix Helix Podcast hosted by Eileen Laird — This is a fantastic, free audio resource that covers all of the facets of the healing process. Podcasts are amazing because you can listen while on your commute, getting some exercise, or cooking dinner. The long format allows time to really go in-depth with some of the concepts I highlighted up above.

Additional Resources

To check out additional resource recommendations, including more AIP-friendly recipe blogs, compliant cookbooks, kitchen gadgets and tools, and other helpful links, click over to the Autoimmune Paleo Resources Page!

I hope you’ve found this guide helpful, and that it has started to get you thinking both about how to educate yourself about your condition as well as some of the areas you can address to live healthier, despite autoimmune disease. Sincerely wishing you the best of luck as you embark on this transformative process!

About Mickey Trescott

Mickey Trescott is a co-founder here at Autoimmune Wellness and a co-teacher of AIP Certified Coach. After recovering from her own struggle with both Celiac and Hashimoto’s disease, adrenal fatigue, and multiple vitamin deficiencies, Mickey started to write about her experience to share with others and help them realize they are not alone in their struggles. She has a Master's degree in Human Nutrition and Functional Nutrition, and is the author of three best-selling books--The Autoimmune Paleo Cookbook, The Autoimmune Wellness Handbook, and The Nutrient-Dense Kitchen. You can watch her AIP cooking demos by following her on Instagram.


  • Agness of Run Agness Run says

    Such great tips! It really helped me find out more and learn new things concerning autoimmune diseases.

  • Mickey & Angie-

    You’re both so wonderful and this website has been such a blessing for me. I’m not currently diagnosed with anything because I’m still trying to pin down my symptoms. My primary care physician, countless dermatologists/allergist keep saying “you’re normal.” As frustrated and lost that I feel, AIP is the only thing that has helped and I’m truly grateful.

    • Angie Alt says

      That’s great to hear! Thanks for sharing that it has been a positive for you, despite still seeking diagnosis.

      • Kacie says

        Mickey, my story is so similar to yours. I’ve been suffering for years now, going from healthy to miserable, and am finally seeing the big picture and getting to the diagnosis of my autoimmune disease. Angie, you know my amazing therapist, who lovingly pointed me in the direction of this beautiful site. Thank you for sharing this gift to wellness with us all. I can’t wait to experience the healing that awaits. With gratitude…

    • Mickey Trescott says

      Hi Aubrey, sorry to hear you are in diagnosis limbo, many of us have spent a considerable amount of time in this space. I’m happy that the info here has been helpful, and that you continue on the road to recovery!

  • Robin says

    I recently have been diagnosed with Hashi’s. I have been reading your blogs, as well as listening to the podcast. Thank you so much for all you do, it has been really helpful.
    I have spent the last 20 years struggling with food allergies, which have continued to increase. My body would become allergic to the modified foods. This has been very discouraging because my non allergy food list has become quite limited. Often these ongoing increased allergies have been to foods that I thought should be healthy for my body, such as avocados, almonds, pineapple, bananas. I have already been egg and dairy free for 10+ years. I am preparing to try the AIP diet and am hopeful after reading so many positive results from others. I have never had gluten identified as an allergy food but after reading how gluten can cause such an imbalance in the gut and overall inflammation, I am hoping to reset my over-reactive system.

    • Mickey Trescott says

      Hey Robin, so happy you are here! I am hoping you have great results with AIP. Wishing you the best.

  • Thanks for the shout-outs, Mickey! I love this article and have it saved for easy reference. I’ve also shared it on Facebook and Pinterest. With the autoimmune epidemic, new people are getting diagnosed every day, and this article will help them feel a lot less scared and alone.

  • Virginie says

    Thank you so much!
    I was diagnosed with Hashimoto’s 2 weeks ago.
    I figured that’s what it was back in November.
    I have a couple of the cookbooks you suggested, but it’s wonderful to read such a nice summary of the situation.
    It’s been very overwhelming trying to figure out the whole meal planning and what I can cook that would fit AIP and low cholesterol dietary requirements ( Yay genetics :/ )
    I’ve loved reading your articles and emails.
    Thank you so much for all the work you all do to help build and grow this community!

    • Mickey Trescott says

      Thanks for being here Virginie, good luck!

  • Jane Messer says

    Hi, just found your great site and was wondering if you have any help and advice. I have Addison’s disease, hypothyroidism, pernicious anemia, vitiligo. Any tips would be greatly appreciated
    Thanks so much

    • Mickey Trescott says

      Hi Jane! Unfortunately we are not medical practitioners and can’t advise on medical conditions. We personally have used the elimination and reintroduction protocol with great success in our own lives and include lots of information about it here on the site. Hope it helps!

  • Emma says

    I’ve been on the AIP diet since September. I’m still in the process of getting a diagnosis and my doctor wants me to have some testing done. But the AIP diet lowered my symptoms a lot, and now I’m scared that the inflammation is too low to get a clear diagnosis. Should I stop the AIP diet a few days before medical testing? I’m scared to do so and suffer again, but I’ve been looking for a clear explanation to my condition for so long that I don’t want to ruin it with my efforts (yes, this is paradoxical ^^). What do you think? Have you already heard about similar stories?

    • Mickey Trescott says

      Hey Emma! Yes, this happens especially with people who have Celiac disease but are unconfirmed, and are told they need to eat some gluten for 1-2 weeks in order to get a positive result. I would have a conversation with your doctor and come up with a plan, because it really depends. If you potentially have an autoimmune disease where a diagnosis will mean more treatment options down the line, it is worth considering. Congrats on your progress, and hope you find a solution that doesn’t involve causing any reactions!

  • tamr says

    Thanks Micky for this informative post, found it on google but it looks like I will be visiting on a daily basis 🙂

  • Tracy says

    Try this one on for size. P Anca Vasculitis. Ever heard of it? Most people including doctors, have not. I am one of the rare 200,000 people on this planet that have it. They aren’t even sure how to treat it. I am fighting it in my own way and doing everything I can to avoid contamination. It is kind of like being isolated for radiology testing. They isolate me every time I go to emergency or the doctor’s office. It is attacking my organs and they Don’t know quite what to do with me and how to treat it. I am fighting every single day against it. Ironically I have become a much stronger person because of it, or maybe in spite of it.

    • Mickey Trescott says

      I’m sorry to hear Tracy! We’ve heard from many who suffer from very rare conditions. Wishing you wellness on your journey and that you find a way to best manage your condition.

    • Kim says

      My daughter was just very recently diagnosed with GPA vasculitis. Please try Cleveland Clinic. She is still there and doing well and they have a full team of doctors taking care of her. Don’t mess around with regional hospitals!! I pray that you can get the treatment needed for this horrible disease! 🙏

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