Background: Hypothyroidism induced by an autoimmune process is associated with neuropsychiatric symptoms and metabolic abnormalities in the brain. The aim of this study was to examine the relationship between autoimmune thyroiditis and regional brain function in hypothyroid patients. Methods: Cerebral glucose metabolism, as an index of brain function, was assessed in regional whole-brain analyses using positron emission tomography (PET) and [¹⁸F]fluorodeoxyglucose in thirteen hypothyroid patients with autoimmune thyroiditis suffering from neuropsychiatric symptoms. The primary biological measures were radioactivity in pre-selected brain regions, relative to whole-brain radioactivity, as a surrogate index of glucose metabolism, and serum levels of thyroglobulin (TG) and thyroid peroxidase (TPO) antibodies as endocrine markers of autoimmune thyroiditis. Results: Serum levels of anti-TG antibodies in hypothyroid patients were significantly correlated with glucose metabolism in the perigenual anterior cingulate cortex, a brain region previously shown to regulate affect and emotional homeostasis. Conclusion: Thyroid autoimmune processes may play an important role in the still poorly defined pathogenic correlates of disturbed function in brain regions critically involved in emotional processing in hypothyroid conditions.