HLA-B*58:01 and HLA-B*57 are protective alleles against human immunodeficiency virus type 1 (HIV-1) subtype B or C infection, whereas these HLA alleles have not been reported as protective in HIV-1 subtype AE infection. Although HLA-B*58:01–restricted and HLA-B*57–restricted HIV-1–specific CD8+ T cells have been thoroughly analyzed in subtype B or C infection, they have been only partially analyzed in subtype AE infection. We identified 6 HLA-B*58:01–restricted subtype AE epitopes in Vietnamese individuals infected with subtype AE. HLA-B*58:01–restricted T-cell responses to Gag epitopes, which may control disease progression in HLA-B*58:01+ and HLA-B*57+ individuals infected with subtype B or C, were not protective in subtype AE infection. These findings suggest that the loss of HLA-B*58:01–restricted T cells specific for some Gag epitopes and/or their reduced ability may account for the lack of protective effects conferred by HLA-B*58:01 in subtype AE infection.