HLA antigens A and B were determined in a group of 41 patients with congenital hypothyroidism and 36 of their mothers. Twenty-nine patients had thyroid dysgenesis of whom 23 were functionally athyreotic, four had ectopic and two had hypoplastic thyroid glands. Twelve patients had thyroid dyshormonogenesis, seven of whom had iodide organification defect. A total of 48 antigens were typed in the A and B loci. The results were analyzed in comparison to 388 normal adult subjects from the general population. The only statistically significant difference was an increase in the frequency of HLA-Bw44(12) (48.8% vs 19.3%, P less than 0.02). The incidence of HLA-Bw44(12) was 44.2% in the mothers. There was a decreased frequency of HLA-B7 in the patients which was not significant.