To investigate whether Major Histocompatibility Complex (MHC) polymorphisms influence either susceptibility to SIV infection or progress to actual disease, rhesus monkeys were subjected to various forms of SIV infection and screened for allelic MHC heterogeneity by means of serological and biochemical methods. Animals that are protected against cell associated virus challenges were those that are SIV vaccinated and which shared a particular MHC class I allele (Mamu-A26) with the donor of the infected cells. Comparisons on the rate of infection to AIDS in SIVmac infected macaques showed that most Mamu-A26 positive animals belong to the group of long time survivors. In our outbred colony, about 25% of the rhesus macaques are positive for the Mamu-A26 serotype. Gel electrophoretic analyses demonstrated that isoelectric point (pI) differences of MHC class I heavy chains correlate with allotyping. In addition, the Mamu-A26 specificity was found to display heterogeneity. These results suggest that particular Mamu-A26 (associated) gene products may have the capacity or quality to induce antigen specific cytotoxic T lymphocyte responses that play a key role in controlling SIV infection or vaccine protection.