Autoimmune thyroid 6-month programme:
MSQ 84 to 7

Presentation & Goals

The client presented with a cluster of thyroid-related, metabolic, neurological and immune-mediated symptoms that had been affecting her quality of life for an extended period. Standard medical management — thyroid hormone replacement — had provided limited improvement in energy and overall wellbeing.

Presenting Symptoms

• Underactive thyroid with confirmed autoimmune activity (elevated TPO & Tg antibodies)
• Chronic anxiety and mood instability
• Persistent fatigue and low energy despite medication
• Gut dysfunction — bloating and digestive discomfort
• Brain fog and poor cognitive clarity
• Weight gain of approximately 1.5 stone
• Persistent dry lips — possible mineral and hydration issues

Laboratory Findings

A comprehensive thyroid and metabolic panel went far beyond standard NHS testing — measuring the full picture of thyroid hormone production, conversion, and autoimmune activity.

• TSH: 5.95 (elevated) — indicating the body was demanding more thyroid output than the gland could provide
• Thyroglobulin Antibodies: >4000 (very high) — confirming active autoimmune attack on thyroid tissue
• TPO Antibodies: 278 (significantly elevated)
• Free T4: 15 pmol/L (low-normal) — insufficient thyroid hormone output
• Free T3: 3.5 pmol/L — impaired T4-to-T3 conversion
• ALP: 137 (raised) — marker of nutritional and metabolic stress
• B12: low-normal; Vitamin D: 42 nmol/L (insufficient)

This multi-layered picture — which standard TSH-only testing would have missed — confirmed a whole-systems approach was needed: targeting immune modulation, nutrient repletion, gut integrity, nervous-system regulation and thyroid physiology together.

The Programme

Autoimmune Protocol (AIP) Diet

The dietary foundation was the Autoimmune Protocol — a nutrient-dense, anti-inflammatory framework designed to reduce immune activation, support gut lining integrity, and calm the autoimmune thyroid process. The focus was on meat, fish, vegetables, sweet potato, bone broth, fermented foods, organ meats and coconut-based alternatives, while removing grains, dairy, legumes, nightshades, nuts, seeds, sugar, alcohol and industrial seed oils.

Targeted Supplement Protocol

• Omega-3 and Phosphatidylcholine for immune modulation and cellular repair
• Prenatal Multinutrient with Hydroxocobalamin B12 injections
• Selenium — foundational for TPO antibody reduction
• Ubiquinol (CoQ10) for cellular energy production
• ADK (Vitamins A, D & K) for immune regulation
• T-Convert for thyroid hormone conversion support
• Adaptogens and electrolytes for adrenal and nervous system support

Advanced Therapeutic Interventions

• Low-Dose Naltrexone (LDN) — autoimmune modulation
• Helminth therapy (HDC) — immune recalibration
• Myo-Inositol — thyroid antibody and insulin support
• Nicotine micro-dose patch — neurocognitive support

Lifestyle & Nervous System

Limbic system retraining, structured breathwork and vagal tone practices, daily movement and light exposure, sleep hygiene, and environmental audit for mould and air quality were all integrated as clinically necessary components — not lifestyle add-ons.

Why This Worked

Standard hypothyroid management replaces the missing hormone — but does nothing to address the antibodies attacking the gland. Every element of this programme was chosen because it directly addresses the autoimmune process at its root: the AIP diet removed intestinal permeability drivers, selenium reduced oxidative damage to thyroid tissue, gut repair reduced the immune activation sourced from the gut-thyroid axis, and nervous system support broke the stress-immune feedback loop that perpetuates autoimmunity. The result was not just symptom relief — it was a genuine shift in the underlying immune pattern.