BACKGROUND/AIMS: Neonatal thymectomy induces autoimmune gastritis in BALB/c (minor lymphocyte-stimulating antigen [Mls]-1b) mice, whereas DBA/2 (Mls-1a) mice are resistant. Resistance has been linked to the Mls-1a locus, which encodes a retroviral superantigen, and to superantigen reactive T cells that express V beta 6+ T-cell receptors. V beta 6+ T cells are known to be deleted in mice expressing Mls-1a superantigens. METHODS: Neonatal thymectomized BALB/c and Mls-1a congenic BALB.D2.Mls-1a mice were analyzed to examine directly the role of Mls-1a self-superantigens and V beta 6+ T cells in autoimmune gastritis. RESULTS: Autoimmune gastritis was detected in thymectomized BALB.D2.Mls-1a mice with high incidence. Autoantibodies to the gastric H+,K(+)-adenosine triphosphatase were present independent of the Mls phenotype in sera of gastritic mice. Severe gastritis had already appeared 1 month after thymectomy in BALB.D2.Mls-1a mice. V beta 6+ T cells were deleted in the stomach lymph nodes of 1-month-old gastritic BALB.D2.Mls-1a mice but could be detected by immunocytochemistry in the stomach lesions. CONCLUSIONS: Endogenous Mls-1a self-superantigens and Mls-1a reactive V beta 6+ T cells are not involved in resistance to autoimmune gastritis in BALB.D2 mice.