Must-Have Autoimmune Lab Tests: How to Get What You Need from Your Doctor

Watch my YouTube video to find out the optimal, functional medicine ranges of conventional lab tests that can provide insight into underlying inflammation or autoimmunity.


For anyone with chronic illness, an individually tailored protocol should be undertaken, customized to biochemical individuality, presenting symptoms, family history, and clinical diagnoses. However, with this caveat in mind, my across-the-board recommendations for four of the most valuable specialized functional medicine tests, to use as a preliminary guide for targeted treatment are as follows:

1) A micronutrient sufficiency test such as Genova NutrEval or the SpectraCell test for vitamin, mineral, and essential fatty acid deficiencies, digestive support, antioxidant status, short-term toxic element exposure, and markers of oxidative stress and cellular damage such as lipid peroxides and 8-hydroxydeguanosine (8-OHdG). 2) A DNA PCR-based Comprehensive Digestive Stool Analysis like those from the Genova GI Effects profile, Biohealth 401H or the Diagnostic Solutions Laboratory GI Map for dysbiosis, parasite infections, pancreatic enzyme sufficiency, fecal fats, occult blood, beta-glucoronidase, secretory IgA (SIgA) and short chain fatty acid production, and markers of gastrointestinal inflammation such as calprotectin, lactoferrin, and eosinophilic protein X (EPX). 3) An Organic Acids Test such as Genova Diagnostics Organix Comprehensive Profile to identify deficiencies in amino acids and micronutrient cofactors for metabolic processes, cellular energy and mitochondrial metabolites, methylation sufficiency, neurotransmitter production, bacterial and yeast overgrowth, and markers for detoxification.

4) An adrenal salivary cortisol index test from a company like ZRT lab or the Precision Analytical DUTCH test to evaluate cortisol secretion patterns and hypothalamic-pituitary-adrenal axis dysfunction, and sex hormone testing from companies like Meridian Valley or the DUTCH test.

Regardless of whether you have an autoimmune disorder such as multiple sclerosis or rheumatoid arthritis, a neurodegenerative disease such as Parkinson's or Alzheimer's, chronic Lyme disease, or postural orthostatic tachycardia syndrome (POTS), these tests will be invaluable in unearthing the root causes of your illness and defining a trajectory for treatment.

Defects in the clinical imbalances listed below, which represent many of the realms addressed within the functional medicine model, can be deduced based on these and other testing modalities.

- Digestion and Assimilation

- Immunity, Defense and Repair

- Mitochondrial Energy Production

- Circulatory or Lymphatic Transport

- Hormonal or Neurotransmitter Communication

- Structural Integrity

- Biotransformation and Detoxification

- Metabolic Derangements

- Psychospiritual, Sociocultural, or Energetic Imbalance

Root Cause Resolution Medicine

Because holistic medicine examines the genetic, biochemical, psychosocial, energetic, and spiritual mediators of dysfunction, which transcend and unite disparate disease entities, the approach is uniform no matter what arbitrary biomedical disease label has been consigned to your identity. For example, two patients with different presenting conditions, such as Addison's disease and Sjogren's syndrome, can both have imbalances in assimilation, manifesting as hypochlorhydria, or low stomach acid, which leads to protein maldigestion and translocation of undigested food antigens across the gut barrier, which in turn elicits an inflammatory response from the immune system (Fasano, 2012).

Likewise, two patients with the same condition can have functional impairments in different arenas. One person with lupus may have derangements in detoxification, leading to increased toxicant burden and multiple chemical sensitivity (MCS). In MCS, chronic, low-level, or acute, high-level exposures to toxicants can result in a two-step process resembling allergic sensitization known as toxicant-induced loss of tolerance (TILT), whereby the levels of chemicals encountered exceed the ability of the body to detoxify and excrete them such that commonplace chemical, drug, food, and alcohol exposures become problematic (Miller, 1997). Or, in a person with detoxification deficits, the covalent binding of chemicals to tissue can take place, creating new immunogenic haptens which lead to tissue damage when the immune system targets the foreign chemical for destruction (Vojdani, 2014).

On the other hand, another patient with lupus, suffering from the exact same symptoms as the patient above, might contend with mitochondrial dysfunction due to enhanced production of reactive oxygen species (ROS), which leads to oxidative damage and interferes with synthesis of cellular energy currency by disrupting the machinery of oxidative phosphorylation within the inner mitochondrial membrane (Zeviar et al., 2014). In most instances, for most patients, given the interconnected nature of the body, each of the spheres of focus listed above must be addressed for healing.

How to Use A Functional Medicine Approach within the Mainstream Medical Paradigm

One of the most frequent gripes, however, that I encounter among autoimmune patients, is that functional medicine is cost prohibitive. Without a doubt, specialized functional testing, such as investigations for chronic inflammatory response syndrome (CIRS), sequencing of genetic polymorphisms, investigations for Lyme and co-infections, and the aforementioned functional tests can constrain finances. Oftentimes, experienced physicians will make clinical diagnoses, treat prophylactically, and use improvements in symptoms as evidence of the suspected disorder. However, in my opinion, gathering anthropometric and laboratory data is of paramount importance for honing the precision of the treatment modalities employed.

Luckily, there are some go-to lab tests, often covered by insurance, that are surrogate markers for underlying autoimmune and inflammatory processes in the body as well as functional imbalances, which can be ordered by an open-minded conventional medical physician. Furthermore, if budget is tight, there is a plethora of actionable data which you can acquire via conventional testing at Quest or LabCorps if ordered by an amenable conventional medical physician. All of the below tests were covered by my insurance, and may or may not be reimbursable or covered depending on your insurance carrier. If your doctor agrees to order any of the following tests, ensure their coverage beforehand to avoid any catastrophic bills.

Personally, I hit the jackpot with my conventional provider, who ordered all of these tests that I requested in one visit---however, this scenario is far from the norm. In fact, if you inundate your practitioner with this list of tests, they are likely to venture into the territory of overwhelm and quickly throw their hands up and show you the door. As previously emphasized, testing should be guided by a licensed medical physician and prioritized based on symptomatology and patient history, heeding budgetary considerations. I also made a YouTube video above to accompany select labs, where I explain conventional inflammatory markers that can reveal an underlying autoimmune process or elevated oxidative stress. Oxidative stress essentially represents an imbalance between the generation of tissue-damaging free radicals and the body's ability to neutralize them via endogenous antioxidant defense mechanisms. As discussed in my introduction to functional medicine post, the allopathic paradigm fails to acknowledge a spectrum from health to disease, instead only recognizing black-or-white overt pathology, whereas functional medicine recognizes gradations of dysfunction and a spectrum from wellness to illness. Since traditional reference ranges were often established based on sick cohorts, conventional medicine has lax reference ranges and often classifies lab results as "normal" even when they indicate aberrant function. Thus, in this video, I provide you with functional medicine ranges, or optimal values, for certain inflammatory markers, for both prevention of disease and for reclaiming vitality. By no means are the tests in this table or video exhaustive or guaranteed to be complete, accurate, up-to-date, or a substitute for functional medicine testing in terms of their specificity or sensitivity. As always, nothing I say is a substitute for medical advice, diagnosis, or treatment of any kind. Please view my disclaimer for more information and consult a licensed physician before applying any information to your case.

I have no financial affiliation or business relationship with any of these companies, but have gleaned priceless information from many of these functional medicine tests. It is important to test, not guess, and to track, because it is difficult to improve upon what is not measured.

Lastly, it is fundamental to educate yourself on the meaning and necessity of these tests before requesting them from an allopathic physician. Functional medicine is characterized by a participatory, egalitarian relationship, where doctor and patient alike embark on a therapeutic partnership to systematically address each facet of chronic illness---and within this model, personal responsibility is a quintessential element. Rather than surrendering your power to a patriarchal and paternalistic medical establishment, empower yourself with knowledge such that you can advocate for yourself and mount a strong argument in favor of the tests you require.

If all else fails, and your doctor refuses your requests, get a second opinion--or visit a direct-to-consumer lab such as My Med Labs, and take back the reigns to your health care management.


Fasano, A. (2012). Leaky gut and autoimmune disease. Clinical Reviews in Allergy and Immunology, 42(1), 71-78.

Miller, C. S. (1997). Toxicant-induced loss of tolerance--an emerging theory of disease? Environmental Health Perspectives, 105(Suppl 2), 445-453.

Vojdani, A. (2014). A potential link between environmental triggers and autoimmunity. Autoimmune Diseases, 1-18. doi:10.1155/2014/437231

Zeviar et al. (2014). The role of mitochondria in cancer and other chronic diseases. Journal of Orthomolecular Medicine, 29(4), 157-166.

#functionalmedicine #autoimmunedisease #labtests #Lymedisease #Hashimotosthyroiditis #hormones #infections #heavymetals #multiplechemicalsensitivity

Follow Me
  • Grey Facebook Icon
  • Grey Twitter Icon
  • Grey Instagram Icon
  • Grey Pinterest Icon