Top Functional Medicine Doctor for Autoimmune Disease in New York City
Autoimmune diseases are rising at an alarming rate. Testing is improving and more doctors are acknowledging that these conditions exist. Yet millions of people continue to be misdiagnosed, dismissed, or left without clear answers. You deserve to work with a doctor who understands autoimmune disease.
Dr. Raphael Kellman, MD, is New York City’s leading functional and microbiome-focused physician. Instead of suppressing symptoms, he identifies the underlying mechanisms driving immune dysfunction, chronic inflammation, gut imbalances, and thyroid abnormalities.
When we address these root causes from a functional medicine perspective, we are able to significantly improve—and in many cases reverse—autoimmune disease.
Autoimmune Disease Treatment Starts with the Microbiome
Autoimmune diseases are frequently overlooked because routine lab tests rarely capture the deeper disturbances happening in the gut, microbiome, and thyroid—the three systems most responsible for regulating immune balance. As a result, many patients spend years struggling with fatigue, pain, digestive discomfort, or thyroid-related symptoms without ever understanding the root cause.
Dr. Kellman takes a distinctly investigative approach, using advanced diagnostics to uncover hidden microbiome imbalances, intestinal permeability, dysregulated gut-immune activity, and subtle forms of thyroid dysfunction that standard testing often misses. By examining these three interconnected systems in detail, he can identify the true biological triggers driving autoimmune activity.
This deeper level of precision allows Dr. Kellman to correct the foundational disruptions—healing the gut lining, restoring microbial diversity, and optimizing thyroid function—so that the immune system can rebalance naturally. Instead of suppressing symptoms, this approach helps patients heal at the root.
What Does It Mean to Have an Autoimmune Disease?
Autoimmune conditions occur when an imbalanced or dysfunctional immune system mistakenly attacks the body’s own healthy tissue. Instead of responding to outside threats such as viruses or bacteria, immune cells begin to target organs, glands, joints, nerves, or the gut lining. This “overactivation” leads to chronic inflammation—often systemic and widespread.
Inflammation is the common denominator in nearly all chronic diseases. Unfortunately, many routine tests miss key inflammatory markers and early autoimmune patterns, leaving patients with persistent symptoms and no clear diagnosis. Functional medicine looks deeper to uncover these hidden imbalances and intervene long before permanent damage occurs.
Six Common Autoimmune Diseases
While autoimmunity can take many forms, these are among the most common conditions Dr. Kellman sees in practice.
Over 80 different conditions—including rheumatoid arthritis, systemic lupus erythematosus, multiple sclerosis, Graves’ disease, and Hashimoto’s disease—fall under the umbrella of autoimmune conditions. While these diseases are often viewed as separate by most doctors, they actually share common root causes.
The Functional Medicine Approach
Specialized Inflammation and Immune Testing
Systemic inflammation is a hallmark of autoimmune disease and many chronic conditions. Dr. Kellman uses advanced laboratory technologies to assess inflammatory markers including CRP, Interleukin-6, IL-8, IL-10, and TNF-α. He also evaluates antioxidant status, a critical measure of true immune resilience.
The Gut–Autoimmune Connection
Don’t underestimate the power of the gut when it comes to autoimmune disease. Autoimmune disease often begins in the gut. A compromised microbiome, leaky gut, or GI dysfunction can create the inflammation and immune confusion that leads to autoimmunity.
Dr. Kellman’s pioneering approach includes a detailed assessment of:
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Microbiome balance
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Bacterial diversity
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Gut permeability
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Digestive function
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Hidden infections
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Short-chain fatty acid production
When you heal the gut, you can profoundly improve—even reverse—many autoimmune diseases.
Thyroid Dysfunction and Autoimmunity
One of Dr. Kellman’s groundbreaking insights is the strong link between autoimmune disease and low thyroid function. Even when routine thyroid panels appear “normal,” many patients still exhibit low thyroid physiology at the cellular level—something traditional testing often fails to detect.
Low thyroid function can worsen autoimmune symptoms, slow healing, and trigger fatigue, hair loss, gastrointestinal issues, and brain fog.
Common Triggers for Autoimmune Conditions
Autoimmunity is rarely caused by one single factor. Instead, a combination of triggers overwhelms the immune system over time. The most common include:
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Viral or bacterial infections
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Toxin exposure
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Chronic stress and anxiety
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Food sensitivities
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Gut microbiome imbalances
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Leaky gut syndrome
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Medications (especially antibiotics)
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Poor diet
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Genetics
Top 8 Symptoms of Autoimmune Disease
Because autoimmune diseases can affect nearly every system in the body, symptoms vary widely. The most frequent include:
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Chronic fatigue
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Joint or muscle pain
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Ggeneralized malaise
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Inflammation or swelling
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Digestive issues
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Rashes or skin problems
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Fever or swollen glands
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Low thyroid function
Autoimmune Treatment Options With Dr. Kellman
Each patient receives a highly personalized treatment plan that integrates functional nutrition, microbiome medicine, advanced therapeutics, and targeted healing technologies. When combined, these modalities can create profound improvements in symptoms, inflammation, and overall health.
Begin Healing Your Autoimmune Disease With Dr. Kellman
Whether you have a confirmed diagnosis or suspect autoimmune dysfunction, you do not need to navigate this alone. Dr. Raphael Kellman offers one of the nation’s most advanced functional medicine programs for autoimmune recovery, and he helps patients restore balance, reduce symptoms, and reclaim their quality of life.