Autoimmune disease is common, frequently slow to diagnose, and often managed in a way that controls the immune response without ever asking what provoked it. Both parts of that sentence matter. Immunosuppression is genuinely valuable medicine. It also isn’t the whole of what can be done.
This guide explains the main autoimmune patterns, what testing is and isn’t capable of, which supportive interventions have evidence behind them, and — importantly — the situations where you need conventional specialist care rather than a functional medicine plan.
Dr. Bronwen Martin, DC, IFMCP and Dr. Andy Martin, MD work with autoimmune patients across San Antonio, Austin, Dallas, and 32 states. The MD credential is relevant here: it means we know where the boundaries are.
Understanding the Basic Pattern
Autoimmune disease occurs when the immune system produces a sustained response against the body’s own tissue. There are more than 80 recognised conditions, and the NIH National Institute of Arthritis and Musculoskeletal and Skin Diseases maintains accessible overviews of the major ones.
The research consensus points to a combination of factors: genetic susceptibility, an environmental trigger, and a loss of immune tolerance. Genes load the gun; something else pulls the trigger. That framing matters clinically, because genes can’t be changed and triggers sometimes can.
Autoimmune conditions also cluster. Having one meaningfully raises the likelihood of another, which is why a patient with Hashimoto’s warrants screening attention for celiac disease and vice versa.
Common Presentations We See
Hashimoto’s thyroiditis is the most frequent autoimmune diagnosis in our practice. Elevated TPO or thyroglobulin antibodies frequently precede TSH abnormality by years, meaning many patients spend a long period symptomatic and undiagnosed. See our thyroid page.
Rheumatoid arthritis presents with symmetrical small-joint pain and prolonged morning stiffness. This requires rheumatology involvement — disease-modifying therapy prevents joint destruction and delay causes permanent harm.
Celiac disease is underdiagnosed and often presents without classic digestive symptoms. Fatigue, anaemia, neurological symptoms, or dermatitis herpetiformis may be the only signs. Critically, serology must be done while still eating gluten. The NIDDK covers this.
Psoriasis and psoriatic arthritis, inflammatory bowel disease, lupus, and Sjögren’s each have distinct patterns and distinct specialist pathways.
If you have a diagnosis and want to understand what sits underneath it, a free 15-minute consultation is a starting point.
Diagnostic Considerations: What Testing Can and Can’t Do
Autoimmune serology is genuinely useful and genuinely limited. Being clear about both prevents a lot of unnecessary anxiety.
Antibody testing — ANA, TPO, tTG-IgA, anti-CCP, and condition-specific panels — is validated and meaningful. But a positive ANA is not a diagnosis. ANA is positive in a substantial proportion of healthy people, and interpreting it without clinical context generates alarm rather than information.
Inflammatory markers — ESR and CRP — indicate activity but not cause.
Antibody levels don’t reliably track symptoms. Some patients improve substantially while antibodies stay elevated. Some see antibodies fall without proportional symptom change. Anyone promising antibody reduction as a guaranteed outcome is overreaching.
Screening for co-occurring conditions is worth doing systematically, particularly celiac serology and a full thyroid panel with antibodies.
Nutrient and inflammatory workup — vitamin D, ferritin, B12, and hs-CRP — informs supportive care and identifies deficiencies that immunosuppressive medication and malabsorption can worsen.
We’re candid that the gut permeability and microbiome testing frequently marketed to autoimmune patients sits on thinner evidence. The gut-immune relationship is real and well-supported mechanistically; the commercial tests claiming to quantify it for individuals are less established. More on our gut health approach.
Evidence-Based Supportive Care
These interventions have reasonable support and work alongside conventional treatment rather than replacing it.
Nutrient repletion. Vitamin D insufficiency is associated with autoimmune activity across multiple conditions and repletion is low-risk. Iron, B12, and folate deficiency are common and correcting them improves fatigue independently of disease activity.
Structured dietary trial. An elimination and reintroduction protocol conducted properly — a defined removal period followed by systematic reintroduction — identifies genuine triggers. Modified autoimmune protocol approaches have preliminary evidence in inflammatory bowel disease and Hashimoto’s. We use structured trials rather than permanent broad restriction, which carries real nutritional risk.
Strict gluten avoidance in confirmed celiac disease. Non-negotiable and the only treatment with definitive evidence.
Sleep and circadian support. Sleep deprivation measurably increases inflammatory signalling.
Stress physiology. The stress-immune relationship is well established. Practical intervention here is neither soft nor optional.
Movement calibrated to disease activity. Appropriate exercise reduces inflammatory markers and improves function. Overtraining during a flare does the opposite.
Smoking cessation, which has among the strongest evidence of anything on this list, particularly for rheumatoid arthritis.
Details of the full protocol are on our autoimmune care page.
When You Need Conventional Specialist Care
This section is the one we most want San Antonio patients to read.
See a rheumatologist or your physician promptly if you have persistent joint swelling with morning stiffness lasting over an hour, unexplained fever with joint or skin involvement, a malar rash, significant unintentional weight loss, new neurological symptoms, breathlessness or chest pain, kidney involvement suggested by urinalysis, or eye pain and visual change.
Do not delay disease-modifying therapy in rheumatoid arthritis while trying dietary approaches. Joint damage in the early window is permanent. Do not stop immunosuppressive or biologic medication without your prescriber’s involvement. Do not start a gluten-free diet before celiac testing.
Functional medicine adds to specialist care in autoimmune disease. It does not substitute for it, and we coordinate with your existing team as a matter of course. Our approach is set out on how we work.
Frequently Asked Questions
Q: Can autoimmune disease be reversed or cured?
A: Remission is a recognised outcome for several autoimmune conditions and is a legitimate goal. Cure is not a claim the evidence supports, and where tissue damage has already occurred — destroyed thyroid tissue, eroded joint surfaces — that damage doesn’t reverse. What can often change is disease activity, symptom burden, flare frequency, and in some cases medication requirement. We’d rather set that expectation clearly at the start than have you discover it at month eight.
Q: Do I need to be in Houston to work with you if I live in San Antonio?
A: No. We’re based in Houston, Texas and see San Antonio patients through HIPAA-secure telehealth, as we do patients in Austin, Dallas, and 32 states. Blood work is done at a lab near you, and appointments are by video. Where you need in-person specialist care — rheumatology, gastroenterology, dermatology — you’ll see someone locally in San Antonio, and we’ll coordinate rather than duplicate.
Q: Will a gluten-free or autoimmune protocol diet help my condition?
A: It depends on the condition and the individual. In confirmed celiac disease, strict gluten avoidance is essential. In Hashimoto’s and inflammatory bowel disease there is preliminary evidence for structured elimination approaches, with meaningful individual variation. In other conditions the evidence is thinner. Our approach is a defined trial with systematic reintroduction so you learn what actually affects you, rather than indefinite restriction based on a general recommendation.
Q: Should I get an ANA test?
A: Only if there’s a clinical reason. ANA testing in the absence of suggestive symptoms produces a meaningful rate of positive results in people who never develop autoimmune disease, and the result then causes considerable worry and often unnecessary follow-up. If you have symptoms that warrant it, it’s a useful test interpreted alongside the full clinical picture. As a general screen, it isn’t recommended.
