Do you treat complex chronic illness for patients outside the Bay Area?

Yes. I see patients with complex, overlapping chronic illness anywhere in California by video. I'm licensed in California, so patients need to be located in the state. If you live outside California, your own doctor can still get my guidance: clinicians can book a one-on-one case consult with me about your care, while they remain your treating physician.

I have several diagnoses. Where do you start?

With the dominant constraint: whatever is limiting your body most right now. For many patients, that means stabilizing the nervous system or mast cells before addressing mold, infections or gut problems. Starting there often makes the next steps tolerable.

I've tried many protocols and feel worse. Can you help?

This is one of the most common reasons people come to me. More treatment isn't always better, especially in a sensitive or depleted system. I review everything you're taking, simplify where I can, and rebuild the plan at a pace your body can handle. If you already have a practitioner and want a second opinion on your plan, a Protocol Review is a good place to start.

Do you treat Lyme disease and other chronic infections?

Yes. I treat Lyme disease and other chronic infections, including other tick-borne infections and viral reactivation, as part of the overall picture. Because their symptoms overlap with mold illness and other conditions, I start with careful screening. In my experience, the large majority of my patients with tick-borne infections see them resolve once the rest of the immune system is supported and its other burdens, such as mold, are addressed, without relying on long kill phases aimed at the organism itself.

What is The Longevity Hierarchy™?

It's a framework I developed for sequencing care according to the body's capacity to respond. It organizes the common drivers of chronic illness into seven levels, from environmental toxins and infections to hormones, the nervous system and mast cells. It guides the order and pace of treatment, so care builds resilience rather than overwhelming the system. It's a theoretical framework, based on my years of clinical experience, though it hasn't yet been externally validated.

How long does it take to get better?

It varies, and healing is rarely linear. Complex illness tends to improve in layers, with setbacks along the way. A flare doesn't necessarily mean you're going backward. Consistency, pacing and a steadier nervous system often matter more than doing everything at once.

Complex Chronic Illness

Functional medicine care for overlapping, multi-system chronic illness, including chronic infections.

I'm Dr. Stephanie Daniel, DO. I founded Functional Medicine SF in 2012. Most of my patients don't have one diagnosis. They have several, and the conditions affect each other. Complex illness is the center of my practice.

Apply for a Welcome Consultation Take the 5-minute Protocol Audit →

Who this page is for

You may have seen many doctors and collected several diagnoses, such as mold illness, MCAS, POTS, SIBO, chronic fatigue, hormone problems or a chronic infection, without anyone explaining how they fit together. Signs that your illness may be complex include:

Symptoms in many body systems at once
Reacting to foods, chemicals, supplements or medications
Feeling worse after treatments that were supposed to help
Good days and bad days with no clear pattern
A long list of supplements and protocols, with less progress than you expected
Being told your tests are normal, or that it's stress or anxiety

Why complex illness is often missed or hard to resolve

Medicine is organized by specialty, so each doctor sees one part of the picture. Many of these conditions also look alike. Mold illness, Babesia and Epstein-Barr virus reactivation, for example, can all cause night sweats, profound fatigue, anxiety, dizziness and insomnia. Without sorting out which drivers are active, treatment can target the wrong one.

Complex illness can also get worse with more treatment. Many of my patients come to me on long lists of supplements and protocols, each reasonable on its own. Together, they can overwhelm a system that is already depleted. I call this the Longevity Bottleneck™: when the demands on the body, including treatment, exceed its capacity to respond, results get worse instead of better. Adding more isn't the answer. The order and pace of treatment are what change.

How I evaluate complex illness

I start by understanding your whole story. Before your first visit, you complete detailed questionnaires, and I review your prior labs, records, and current supplements and medications. From there, I focus on finding the dominant constraint: the factor that is limiting your body most right now. Testing is chosen to answer specific questions, not to test everything at once. Depending on your history, it may include:

Mold and mycotoxin testing, plus a home assessment
Mast cell and histamine evaluation
Comprehensive stool, organic acids and breath testing
Hormone, thyroid, nutrient and metabolic labs
Nervous system and sleep questionnaires
Screening for chronic infections, starting with validated symptom questionnaires before specialty lab testing

How I sequence treatment

My approach follows The Longevity Hierarchy™, a framework I developed for organizing care around what your body can tolerate right now. It has two aims: reduce the load your body is carrying, and expand its capacity to handle treatment.

The hierarchy has seven levels. The lower four are sources of load:

Biotoxins such as mold and mycotoxins
Total toxic burden, including metals, microplastics and hormone-disrupting chemicals
Microbiome imbalances in the gut and sinuses
Hidden infections, such as viral reactivation or tick-borne infections

The upper three are the body's adaptive systems, which often need stabilizing first:

Hormones, including stress hormones, thyroid and sex hormones
The autonomic nervous system
Mast cells

I work in both directions at once: reducing load from below while stabilizing from above. Not every patient needs every level. When your capacity is low, I simplify and stabilize, and I address load only at a pace you can tolerate. As your capacity grows, treatments you couldn't tolerate before often become possible. With chronic infections, I usually address mold, fungal overgrowth and immune regulation first. Some infections, such as tick-borne ones, may need treatment alongside those steps.

Conditions I treat

Each of these has its own page with more detail:

I also treat autoimmune conditions, heavy metal and chemical toxicity, and dental sources of inflammation such as cavitations, and I support patients with neurodegenerative conditions.

What working with me looks like

A 20-minute welcome consult to talk through your situation and see whether my practice is a good fit.
A 90-minute first visit. I review your history, records and current regimen, identify the dominant constraint, and set out a testing plan.
A written plan that maps out your next steps, with clear instructions and handouts. You put it into practice one change at a time, at a pace your body can handle.
60-minute follow-up visits to review results and adjust the plan as your capacity changes.
Coaching between visits, which is part of my care program. This includes patient support, nutrition and detox coaching to help you put your plan into practice, plus nervous system work such as brain retraining coaching and Depth Hypnosis.
A patient portal for questions, updates and sharing results.

Frequently asked questions

Do you treat complex chronic illness for patients outside the Bay Area?: Yes. I see patients with complex, overlapping chronic illness anywhere in California by video. I'm licensed in California, so patients need to be located in the state. If you live outside California, your own doctor can still get my guidance: clinicians can book a one-on-one case consult with me about your care, while they remain your treating physician.
I have several diagnoses. Where do you start?: With the dominant constraint: whatever is limiting your body most right now. For many patients, that means stabilizing the nervous system or mast cells before addressing mold, infections or gut problems. Starting there often makes the next steps tolerable.
I've tried many protocols and feel worse. Can you help?: This is one of the most common reasons people come to me. More treatment isn't always better, especially in a sensitive or depleted system. I review everything you're taking, simplify where I can, and rebuild the plan at a pace your body can handle. If you already have a practitioner and want a second opinion on your plan, a Protocol Review is a good place to start.
Do you treat Lyme disease and other chronic infections?: Yes. I treat Lyme disease and other chronic infections, including other tick-borne infections and viral reactivation, as part of the overall picture. Because their symptoms overlap with mold illness and other conditions, I start with careful screening. In my experience, the large majority of my patients with tick-borne infections see them resolve once the rest of the immune system is supported and its other burdens, such as mold, are addressed, without relying on long kill phases aimed at the organism itself.
What is The Longevity Hierarchy™?: It's a framework I developed for sequencing care according to the body's capacity to respond. It organizes the common drivers of chronic illness into seven levels, from environmental toxins and infections to hormones, the nervous system and mast cells. It guides the order and pace of treatment, so care builds resilience rather than overwhelming the system. It's a theoretical framework, based on my years of clinical experience, though it hasn't yet been externally validated.
How long does it take to get better?: It varies, and healing is rarely linear. Complex illness tends to improve in layers, with setbacks along the way. A flare doesn't necessarily mean you're going backward. Consistency, pacing and a steadier nervous system often matter more than doing everything at once.

Next steps

Book a 20-minute welcome consult to see whether we're a good fit.
Not sure where to start? Take the 5-minute Protocol Audit to see which areas may be adding to your symptoms.
Already on a protocol that isn't working? A Protocol Review looks at what you're doing and what might be holding you back.

Apply for a Welcome Consultation

Functional Medicine SF provides virtual care for patients located in California. This page is for education and is not individual medical advice.