HLA‐A, B and C antigens tested in 97 patients treated for congenital hypothyroidism, and in members of their families, are compared with normal frequencies from 635 controls. After adjustment for the number of tests, there remains in the patients only a negative association with A11, with a relative risk of 190, and no significant association in the relatives. Patients show no excess homozygosity and no deviations in haplotype frequency. Congenital hypothyroidism thus appears to show a different relationship with HLA from other thyroid disorder