Alopecia areata (AA) is a T cell mediated disease directed against hair follicles that results in bald patches. It can range in severity from patchy (AA), to total scalp hair loss (alopecia totalis; AT) or body hair loss (alopecia universalis; AU). We have previously shown that HLA-DR4 and DR11 as well as HLA-DQ*03 alleles are increased in unrelated AA patients compared with controls. To study whether class II HLA alleles are linked to AA, we investigated 81 extended families that included 192 AA patients, including 89 with AT or AU. We also performed the transmission disequilibrium test (TDT) in 143 nuclear families. Results showed an association between alleles of HLA-DQB (p = 0.014) and HLA-DR (p = 0.010). We also performed linkage analysis in 75 families whose members' genomic DNA were available for HLA typing. Results from this analysis support linkage between AA and class II loci with a maximal LOD score of 2.42 to HLA-DQB at 5% recombination, and with a maximal LOD score of 2.34 to HLA-DR at 0% recombination. There was an increased incidence of atopic dermatitis and autoimmune thyroiditis in families. AA appears to be a class II HLA restricted organ specific immune response to the hair follicle.