What should you do if you think you have an autoimmune disease? 

General Health

written by:

Kayla Martin, MS, CNS

Navigating life with an autoimmune condition can be a confusing and sometimes disheartening experience, characterized by obstacles that extend beyond the physical symptoms. The journey to receiving a diagnosis can be long, hard and sometimes full of self-doubt and uncertainty. 

But we’ve seen countless stories of strength, perseverance, and daily triumphs in those living with autoimmune disorders. 

The prevalence of autoimmune conditions is on the rise in the United States, with an estimated 8% of the population living with autoimmune disorders; 80% of those cases are women. Autoimmune conditions are chronic and difficult to diagnose and treat. They expose the pitfalls of conventional medicine and reveal the importance of integrative, holistic medicine for caring for people suffering from autoimmune disorders. 

At Birchwell, our approach to managing these conditions extends beyond conventional practices – we seek to humanize the experience and empower you to take an active role in your well-being. 

In this article, we delve into the holistic framework and multifaceted steps that we take to manage autoimmune conditions. From dietary adjustments and gut health considerations, to addressing nutrient deficiencies, sleep, stress, and environmental factors, we’ll support you from every angle. We prioritize your physical health and recognize the integral connection between mental and emotional well-being in the pursuit of a more balanced, vibrant life, despite the challenges posed by autoimmune conditions.

What is an autoimmune disorder? 

The immune system is a complex network of white blood cells, antibodies, tissues and organs that work together to defend the body against harmful invaders such as bacteria, viruses and pathogens. 

A healthy immune system protects the body from diseases and infections by identifying which cells are our own and which cells are foreign and potentially harmful invaders. 

However, when the immune system goes awry, it can mistakenly target healthy cells, tissues, and organs in what’s known as an autoimmune disorder. Basically, the immune system isn’t able to differentiate between our own cells and the invaders, leading it to attack our own healthy tissues, organs and cells. 

The most common autoimmune diseases in the United States include: 

  • Rheumatoid Arthritis (RA) 
  • Systemic Lupus Erythematosus (SLE) 
  • Hashimoto’s Thyroiditis 
  • Type 1 Diabetes 
  • Celiac Disease 
  • Psoriasis 
  • Multiple Sclerosis (MS) 
  • Inflammatory Bowel Disease (IBD) 
  • Sjögren’s Syndrome 

How To Tell If You Have An Autoimmune Disorder 

When the immune system gets mixed up and attacks our own cells and tissues, it can result in a cascade of symptoms. The symptoms vary depending on which autoimmune disorder you have and which tissues are affected. 

The most common symptoms of an autoimmune disorder affect the endocrine system (primarily the thyroid), joints, skin, blood vessels, pancreas, central nervous system, eyes, kidneys and lungs, and digestive tract. 

Some autoimmune disorders are organ specific, meaning the immune system attacks a single organ. For example, the thyroid is targeted in Hashimoto’s thyroiditis and the pancreas in Type 1 Diabetes. Other autoimmune disorders are systemic, meaning they impact many organs at once like in Systemic Lupus and Multiple Sclerosis. 

People who have one autoimmune disorder are at an increased risk of another and approximately 25% of people with one autoimmune condition will develop a second. 

Common symptoms include: 

  • Persistent and unexplained fatigue 
  • Joint pain and stiffness 
  • Achy muscles 
  • Skin issues – rashes, redness, 
  • Digestive problems – abdominal pain, diarrhea 
  • Brain fog 
  • Recurring fever 
  • Swelling and inflammation  
  • Swollen glands or lymph nodes 

What causes an autoimmune disorder? 

The cause of autoimmune disorders remains unclear and varies based on the disorder. Some people are predisposed to autoimmune disorders that are then activated by a number of triggers like environmental toxins, poor diet and lifestyle, inactivity, excess stress and poor sleep. 


Women are twice as likely to have an autoimmune disorder than men and the onset often occurs during times of excess stress like pregnancy or other big hormonal shifts. Hormonal shifts during puberty and pregnancy can be the catalyzing event for an autoimmune disorder.


Some people have a higher genetic predisposition for developing autoimmune disorders, although it varies depending on the specific disorder. Crohn’s disease and Rheumatoid arthritis have a high genetic association, while systemic sclerosis has almost none. 


There seems to be an association between ethnicity and autoimmunity as well, although the relationship between the two varies greatly depending on the condition. For example, African Americas are at a higher risk of lupus than European Americans, but a much lower risk of multiple sclerosis. 

Environmental Exposures 

Environmental exposure to heavy metals, pesticides, air pollution, tobacco smoke, food additives, and a number of toxic chemicals found in personal hygiene products, cleaning supplies and makeup are associated with autoimmune disorders. These toxins increase oxidative stress and inflammation which is likely the mechanism by which they influence autoimmune disorders. 


Stress seems to be a major factor when it comes to autoimmune disorders, especially in women. When our bodies are under excess or chronic stress, the nervous system can become activated, dysregulating the immune system and impairing the body’s ability to respond to inflammation. Over time, this can lead to an overactivated immune system and increase the risk of autoimmune disorders.


For many individuals, the instigating event for their autoimmune disorder is an infection. Bacterial, parasitic and fungal infections are associated with autoimmune disorders – but the definitive link, and the strength of that association, depends on the specific condition. 

The majority of the immune system is found in the gut microbiome and when an infection enters the gut, it can alter the immune system. Additionally, certain infections can look like healthy cells to the body, leading the immune system to accidentally attack those cells. We call this phenomenon molecular mimicry since the two compounds (virus and healthy cells) look similar to the body. 

Gut Health 

Since so much of the immune system is made in the gut, the gut microbiome can play an important role in autoimmunity. Different bacteria in the gut support immune cell development and help modulate inflammation, so it’s important we have enough of those bacteria. 

Leaky gut is another major variable in the development of autoimmune diseases. The lining of the gut is designed to allow water and nutrients in, but keep food particles, toxins, and microbes from leaving the intestines and circulating outside of the body. If the lining of the gut becomes permeable or “leaky”, these particles can escape and trigger an immune response.  

Poor Diet Quality 

The prevalence of autoimmune conditions is much higher in Western countries where the Standard American Diet (SAD) is adopted. Common themes of SAD include high calorie, carb and inflammatory fat intake with inadequate consumption of fiber, anti-inflammatory fats, and micronutrients. Dietary factors influence the immune system, gut barrier, and overall inflammation in the body, all of which impact autoimmunity.

How do people get diagnosed with an autoimmune disorder?  

Since the symptoms of autoimmunity can be vague, they’re often misattributed to other factors or diseases. It can take years and multiple practitioners before individuals struggling with autoimmune conditions receive a diagnosis. 

If you think you may be dealing with an autoimmune condition, the first step is to consult with your doctor. There are certain blood tests that can indicate the possibility of an autoimmune disease. 

Depending on your symptoms, your doctor may consider specific tests. For example, symptoms of hypothyroidism may lead to a comprehensive thyroid panel with thyroid antibodies to screen for autoimmune thyroid conditions. 

If you’ve already met with your doctor and they brushed off your concerns as no big deal, it may be time to consider working with a functional medicine practitioner. You should feel heard and like your health matters to your healthcare providers.

Conventional Testing for Autoimmune Disorders  

Consult with your doctor about how to get tested for an autoimmune disorder. Usually, your doctor will conduct a physical exam and choose tests depending on those results. Your doctor will likely start by running a few common tests, including: 

  • Complete blood count with white blood cell differential – to determine immune activation, presence of infection or inflammation, blood abnormalities and to rule out other conditions that can mimic autoimmunity   
  • Comprehensive metabolic panel – not a specific test for autoimmunity, but it does provide clues about potential autoimmune disorders, especially those related to the liver, kidney and pancreas function, electrolyte imbalances, and glucose levels. 
  • Erythrocyte sedimentation rate (ESR) – to assess inflammation (note, not all traditional primary care providers will include this test). 

Functional Medicine Testing for Autoimmune Disorders 

Functional medicine tests can help provide information about the underlying cause of autoimmunity and why the immune system is going haywire. Some of the tests we may run at Birchwell include: 

Antinuclear antibody tests (ANA)

Antinuclear antibodies are a type of autoantibody associated with autoimmunity. ANA, or antinuclear antibodies, are antibodies that target the nuclei of cells. A positive ANA test indicates the presence of these antibodies in the blood and is often ordered when there is suspicion of an autoimmune disorder.  

C-reactive protein (CRP)

C-reactive protein is a test to assess inflammation. CRP is produced by the liver in response to inflammation. Inflammation is a common feature of autoimmune diseases. Elevated CRP suggests the presence of inflammation, prompting further investigation into the root cause. CRP levels can be used to monitor the activity of certain autoimmune diseases, such as rheumatoid arthritis and lupus since changes in CRP over time may indicate fluctuations in disease activity. Monitoring CRP levels can also be useful in assessing how well a patient is responding to treatment. It’s important to note that while CRP is a valuable marker of inflammation, it is not specific to autoimmune diseases. Elevated CRP levels can be seen in various other conditions, including infections, trauma, and other inflammatory disorders.

Thyroid-peroxidase antibodies and thyroglobulin antibodies 

These antibodies are specifically associated with autoimmune thyroiditis. These antibodies play a key role in the diagnosis of autoimmune thyroid diseases, particularly Hashimoto’s thyroiditis and Graves’ disease. Elevated levels of these antibodies provide evidence of an autoimmune process affecting the thyroid gland. Additionally, monitoring these antibody levels over time can help assess the progression of the autoimmune response and the effectiveness of treatment. 


The GI MAP is an advanced diagnostic stool test to analyze the gut microbiome, identifying pathogens, beneficial bacteria, and potential imbalances. The health of the gastrointestinal (GI) tract is closely linked to the immune system and gut dysbiosis has been associated with various autoimmune conditions. A healthy gut may contribute to immune system balance, and identifying and addressing gut-related issues with the GI MAP can be part of a comprehensive approach to managing autoimmune conditions.

Environmental Toxins, Mold and Heavy Metals 

Exposure to environmental toxins, mold, and heavy metals can potentially contribute to chronic inflammation and immune system dysregulation. Chronic exposure to these elements may trigger or exacerbate autoimmune conditions in susceptible individuals. Testing for these toxins may provide information about potential contributors to inflammation and immune system dysfunction, offering information about the root cause. We use this information to create a targeted plan to minimize your exposure and optimize your body’s natural detoxification processes. 

Array 5 Autoantibodies 

The Array 5 test is designed to assess immune reactivity to multiple antigens. It includes testing for antibodies against various tissues and proteins, allowing for a broad evaluation of autoimmune reactivity. Identifying specific autoimmune reactivity patterns helps us understand the root cause of immune activation.  

If you have a confirmed autoimmune disease that requires medication management, we’ll help connect you to a specialist that’s an expert in your specific condition. Unfortunately, that doctor likely won’t have the time to address the root cause and approach your health holistically. But, that’s where we come in!  

What to do if you find out you have an autoimmune disease? 

Take a holistic approach to healing your autoimmune disease! Consider these variables to begin addressing your new diagnosis. 


The cornerstone of managing autoimmune conditions lies in adopting an anti-inflammatory and personalized diet. Removing potential triggers such as gluten, dairy, and processed foods can alleviate symptoms. Additionally, incorporating foods rich in antioxidants, omega-3 fatty acids, and a variety of colorful fruits and vegetables can promote detoxification and combat inflammation. 

Emerging evidence suggests that heavy metals and certain pathogens may contribute to autoimmune disorders. Therefore, focusing on a diet that supports detoxification pathways and includes foods with chelating properties, such as cilantro and chlorella, can be beneficial.

Identifying and correcting nutrient deficiencies is crucial for optimal immune function. Comprehensive testing can pinpoint deficiencies, allowing for targeted supplementation. Common deficiencies in autoimmune conditions include vitamin D, B vitamins, zinc, and omega-3 fatty acids. Incorporating nutrient-dense foods and high-quality supplements can address these deficiencies, promoting overall health and supporting the immune system. 

Gut Health 

The gut plays a pivotal role in autoimmune conditions, with a strong link between gut health and immune function. Prioritizing gut healing is essential. Implementing a diverse range of fiber-rich foods, prebiotics, and probiotics supports a healthy gut microbiome. These elements help regulate immune responses and improve the integrity of the gut lining, reducing the likelihood of leaky gut syndrome, which is often associated with autoimmune disorders.

Gluten and Dairy 

Gluten and dairy are two very common triggers for autoimmune disease due to their potential to induce inflammation and disrupt the delicate balance of the immune system. There are proteins in gluten that can initiate an immune response in susceptible individuals, particularly those with celiac disease or non-celiac gluten sensitivity. This immune response can contribute to chronic inflammation and, in some cases, trigger autoimmune reactions. 

Similarly, dairy products contain proteins like casein and whey that have been implicated in immune system disturbances. Some people develop sensitivities or allergic reactions to these proteins, leading to inflammation and potentially contributing to autoimmune conditions. 

The molecular mimicry hypothesis suggests that certain protein structures in gluten and dairy resemble the body’s own tissues, leading to a misguided immune response that attacks both the ingested proteins and similar tissues in the body, creating an environment conducive to autoimmune disease. While not everyone with autoimmune conditions is affected by gluten or dairy, the elimination of these common dietary triggers is often a good first step in managing autoimmune diseases, reducing inflammation, and supporting overall health.


Quality sleep is a non-negotiable aspect of autoimmune management. During sleep, the body undergoes crucial repair processes and adequate rest is essential for immune regulation. Establishing a consistent sleep routine, creating a conducive sleep environment, and practicing relaxation techniques contributes to better sleep hygiene. Prioritizing seven to eight hours of uninterrupted sleep fosters recovery and resilience against the inflammatory processes associated with autoimmune conditions.


Chronic stress is a significant trigger for autoimmune flare-ups since it disrupts the balance of the immune system. Incorporating stress-management techniques, such as mindfulness, meditation, yoga, and deep breathing exercises, can help modulate the stress response. Creating a supportive social network, setting realistic goals, and establishing boundaries are also vital components in mitigating stressors that may exacerbate autoimmune symptoms.

Environmental Toxins 

Reducing exposure to environmental toxins is imperative for autoimmune management. This involves scrutinizing personal care products, choosing organic produce when appropriate, and being mindful of inorganic pollutants. Employing air and water purifiers, avoiding wearing shoes indoors, maintaining a clean environment, and periodically opening windows all contribute to a cleaner living environment, minimizing potential triggers for autoimmune reactions. Reference the Environmental Working Group (EWG) consumer guides to make decisions about which beauty products to use and when to purchase organic produce. We help our clients reduce their toxin exposure gradually and can recommend specific products and changes as needed. 


Supplementation should be tailored to your specific autoimmune disorder and unique needs. Vitamin D supplementation is often crucial, given its immunomodulatory effects. Omega-3 fatty acids can help balance inflammation, while certain autoimmune conditions may benefit from targeted supplements, such as curcumin for its anti-inflammatory properties or probiotics for gut health. Working with a qualified healthcare professional is essential to determine the appropriate supplements based on your unique circumstances and the nature of your autoimmune condition.

Don’t disregard your mental health! 

Amidst the various holistic approaches to managing autoimmune conditions, the significance of prioritizing mental health cannot be overstated. Chronic illnesses, including autoimmune disorders, often take a toll on mental well-being. Integrating strategies such as therapy, support groups, or mindfulness-based interventions not only helps individuals cope with the emotional challenges associated with autoimmune conditions but also positively influences the overall disease trajectory. 

Ignoring mental health can exacerbate stress, potentially triggering autoimmune flares. Incorporating activities that promote mental and emotional resilience, such as regular exercise, artistic expression, and spending time in nature, fosters a holistic approach to well-being. Acknowledging the intricate connection between mind and body is fundamental in achieving comprehensive management of autoimmune conditions.

What if all your tests are negative but you still feel bad? 

Receiving persistently negative test results despite experiencing ongoing health challenges can be an incredibly frustrating scenario. Autoimmune conditions often present a diagnostic challenge, since some people have symptoms indicative of these disorders despite negative conventional test results.

In these cases, we encourage you to consider alternative testing methods and working with a functional medicine practitioner (like us!) to explore comprehensive assessments that delve deeper into immune function, gut health, and potential environmental triggers. Additionally, your symptoms may be subtle or intermittent, requiring a nuanced clinical evaluation that goes beyond standard laboratory results. Collaborating closely with our team to investigate the root causes, implement personalized diagnostic approaches, and develop targeted interventions can offer valuable insights and pave the way for more effective management strategies, even in the absence of positive test results.

The bottom line is that your symptoms matter more to us than your test results. If you continue to receive negative test results but still feel like something isn’t right, we’ll keep digging until we uncover the root cause of your discomfort – and we’ll be your number one advocate for healing every step of the way. 


Feeling better is possible. Meet with one of our practitioners to find out if 1:1 Functional Medicine Consulting is right for you.

Book a complimentary discovery call

Anya is a Registered Dietitian, Functional Medicine Practitioner and founder of Birchwell, a virtual integrative health clinic based in New York City.

She specializes in helping her clients identify the root cause of their health concerns through advanced lab testing and her comprehensive assessment. She uses functional diet, supplement, and lifestyle strategies to address any imbalances in the body. Through her integrative and functional nutrition practice, Anya has helped hundreds of adult women and men fix their gut health (e.g. SIBO, reflux, candida, etc.), balance their hormones (e.g. PCOS, peri-menopause, estrogen dominance, etc.), clear their acne or eczema, boost their energy and performance, combat anxiety and depression, improve their body composition, reduce their joint pain - and more.

Anya Rosen, MS, RD, LD, IFNCP, CPT

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