Mouse experimental autoimmune thyroiditis (EAT), a model for Hashimoto’s thyroiditis, is induced by immunizing with mouse thyroglobulin (MTg). To study the extent of H2A involvement in EAT, we introduced AaAb genes from susceptible k mice into resistant or intermediately susceptible strains which do not express H2E molecules. Thyroiditis was severe in resistant B10.M (H2 ^f ) mice carrying the double transgene Aa ^k Ab ^k . Likewise, thyroid infiltration was significantly extended in intermediate B10.Q (H2 ^q ) mice with the same transgene. To examine the effect of H2E molecules in the presence of H2A-mediated susceptibility, we introduced an Ea ^k transgene into E^– B10.S mice to express the Eβ^s molecule and observed significant reduction in EAT severity in B10.S(E⁺) mice. On the other hand, the presence of an Eb ^d transgene in B10.RQB3 (H2A ^q ) mice resulting in the expression of H2Eβ^d molecules did not alter EAT susceptibility, suggesting a role for Eb gene polymorphism in protection against EAT. We have shown recently that the HLA-DRB1 ^* 0301 (DR3) transgene conferred EAT susceptibility to B10.M as well as class II-negative B10.Ab⁰ mice. However, we report here that the HLA-DQB1 ^* 0601 (DQ6b) transgene in B10.M or HLA-DQA1 ^* 0301/DQB1 ^* 0302 (DQ8) transgene in class II-negative Ab⁰ mice did not. These studies show the differential effects of class II molecules on EAT induction. Susceptibility can be determined when class II molecules from a single locus, H2A or HLA-DQ, are examined in transgenic mice, but the overall effect may depend upon the presence of both class II molecules H2A and H2E in mice and HLA-DQ and HLA-DR in humans.