The presence of circulating autoantibodies (Abs) to the thyroid antigens thyroid peroxidase (TPO) and thyroglobulin (Tg) is a marker for autoimmune thyroid disease. Recent studies have suggested that the tendency to produce these Abs is inherited as an autosomal dominant characteristic. In order to confirm or refute these observations, we have carried out a complex segregation analysis using POINTER on Ab data in 86 unselected pedigrees (172 nuclear families). The overall prevalence of TPO Ab was 9.9% in men and 24.1% in women. Tg Ab was found in 11.0% of men and 23.5% of women. There was a marked tendency for both TPO Ab and Tg Ab to cluster in families and complex segregation analysis provided strong evidence for vertical transmission. However, it was not possible to distinguish between a single locus and a multifactorial model for either Ab. In the absence of strong evidence for a single locus, genetic linkage strategies are unlikely to be successful.