Autoimmune disorders

Autoimmune disorders happen when a child's immune system turns against the body's own tissues, and in children the effects reach beyond fatigue, aches or low-grade fever: they can show up as sudden changes in mood, attention, movement or behavior. At WIN in Houston and San Juan, we look for the immune, infectious and inflammatory causes behind these changes, treat them with functional medicine and nutrition, and then stimulate development once the child has stabilized.

What are autoimmune disorders in children?

An autoimmune disorder is a condition in which the immune system, designed to fight infections, mistakenly attacks healthy cells. The result is chronic inflammation that can affect joints, skin, the thyroid, the digestive tract and, in some children, the brain, producing symptoms that look psychiatric or neurodevelopmental rather than "medical."

Families come to WIN with concerns such as thyroid autoimmunity, celiac disease and inflammatory conditions of the gut, as well as suspected PANS/PANDAS, in which an infection appears to trigger an abrupt onset of obsessive-compulsive symptoms, tics or anxiety. WIN evaluates for these conditions as part of a complete medical workup.

An autoimmune disorder is not a food allergy or a weak immune system. The immune system is not failing; it is overactive and misdirected, and that distinction shapes how we treat it.

Early signs parents notice

Autoimmune activity rarely announces itself clearly. Parents more often describe a child who "changed" over days or weeks, sometimes right after a sore throat, a virus or another illness.

• A sudden, dramatic shift in behavior or personality that seems to come out of nowhere
• New obsessive-compulsive symptoms: repeated hand-washing, checking, intrusive fears, rigid rituals
• Tics, repetitive movements or unusual eye-blinking that were not there before
• Separation anxiety or nighttime fears out of proportion to the child's age
• Regression in skills already mastered: handwriting, toileting, speech or independence
• Refusing foods or eating far less
• Bedwetting after being dry at night
• Fatigue, joint or muscle aches, headaches or recurring low-grade fevers
• Trouble falling asleep, night waking, nightmares

If several of these appear together, or your child regressed noticeably after an infection, request a medical evaluation rather than waiting to see whether it passes.

What causes autoimmune disorders, and why that matters for treatment

Research points to a combination of genetic predisposition and environmental triggers. An infection, chronic exposure to toxins, nutritional deficiencies or a disrupted gut can each push a susceptible immune system toward attacking the body. In PANS/PANDAS, the leading hypothesis is that antibodies produced against an infection cross-react with parts of the brain that regulate movement and behavior.

This is why a diagnosis alone is not enough. Two children with the same label may have different drivers: an untreated infection, an inflamed gut with food sensitivities, or a genetic variant that affects how the body handles inflammation. WIN evaluates for each of these, because the protocol follows the cause, not the label. Calming the immune system first also makes later therapies more effective, since a brain under active inflammation struggles to learn.

How WIN evaluates autoimmune disorders

Evaluation begins in Phase I with the three-part initial medical evaluation: about 1 to 1.5 hours with Dr. Báez-Franceschi and roughly 3 hours in the office. She reviews the full history, with particular attention to the timeline of symptoms, prior infections, antibiotic use and family history of autoimmunity, and performs medical and neurodevelopmental testing.

Specialized laboratories follow. For suspected autoimmune activity these commonly include inflammation and immune markers, testing for active or past infections, gut assessment, a food allergy panel, nutritional deficiencies, metabolic and hormone panels (including thyroid), and genetic testing when indicated. Results are reviewed at the follow-up appointment, where the first protocol is written.

In Phase II, the WIN neurodevelopment evaluations document how the condition has affected development. The primitive reflex test and the Franceschi Method development test matter most when a child has regressed, because they show which skills were lost and where to rebuild; the listening test (CAPD) and tympanogram complete the picture. Parents leave with a written, individualized treatment protocol.

How we treat autoimmune disorders: the three phases

Phase I — Evaluation and planning. The initial evaluation, specialized labs and follow-up appointment identify the immune, infectious and inflammatory factors at work. If an infection or acute condition requires conventional medication, it is treated; medication is part of the plan when needed.

Phase II — Evaluation results and protocols. Medical and nutritional protocols come first, built directly on the labs: a functional medicine protocol for infections, inflammation and gut health, a nutrition plan that removes identified food sensitivities and adds anti-inflammatory foods, and individualized supplementation to correct deficiencies. The WIN neurodevelopment evaluations then shape the treatment protocol discussion.

Phase III — Multisensory and psycho-emotional therapy. As the child stabilizes medically, therapy begins. Behavioral health supports the child and family through anxiety, compulsions and the emotional toll of a sudden change; neurofeedback trains regulation and attention; the sensory room helps a dysregulated nervous system reorganize. Progress is measured constantly, and parents receive reports and training as part of the team. The full approach is described on the Franceschi Method® page.

What families can expect

The first weeks are medical: the initial evaluation, labs, and the follow-up visit where the protocol is explained. Lab review and many follow-ups can be done by telemedicine for families in Texas, Florida and Puerto Rico; international families travel to Houston or San Juan for the in-person evaluation and therapy.

Early progress, when it comes, usually looks like a calmer, better-sleeping child with fewer flare-ups, followed by gradual return of skills. The course varies with each child and with how long the immune process has been active. Parents keep the diet, track symptoms and flares, and report what they see so the protocol can be adjusted.

If your child changed suddenly and no one has looked for a medical reason, we would like to help you find it. Request an orientation with WIN in Houston or San Juan, in English or Spanish. Contact us to begin.