In the light of the diversity of HIV, matching the genotype of candidate HIV vaccines with the transmitted genotype may be required. Alternatively, matching the immunotype of HIV vaccines and transmitted subtypes may be the best option. Since studies of cross-subtype HIV-1 immunity are limited, subtype B specific cytolytic T lymphocyte (CTL) responses were measured in subtype C infected individuals. HIV-1 subtype B-specific CTLs, plasma viral load and absolute CD4 and CD8 lymphocyte numbers were measured in six HIV-1 subtype C infected individuals within a year of seroconversion. HIV-1 subtype B env. gag and nef-specific CTL precursor frequencies were measured by limiting dilution analysis. Three of the six subjects had demonstrable CTL directed at more than one HIV-1 subtype B antigens. One individual demonstrated CTL directed against all three HIV-1 subtype B antigens, while two individuals did not demonstrate CTL against HIV-1 subtype B antigens. The frequencies of CTL precursor were not associated with plasma viral load or absolute CD4 cell counts in peripheral blood. These findings suggest that some individuals recently infected with subtype C HIV-1 generate cross-reactive CTL that are directed against HIV-1 subtype B.