Prior immunity to HIV-1 elicited by vaccination may modify subsequent responses upon exposure to infectious HIV-1. An HIV-1-uninfected person entered in a vaccine trial that included immunizations to HIV-1(LAI) envelope with a recombinant vaccinia vector and recombinant protein developed envelope-specific CD4+ T cell responses, including proliferative and cytolytic responses, but was not protected from a high risk HIV-1 exposure. CD4+ T cell clones derived from blood at the peak of vaccine-induced immunity recognized and lysed autologous target cells expressing four distinct regions within the HIV-1(LAI) envelope region; three of these CTL clones also recognized targets expressing envelope from a similar viral subtype, HIV-1(MN). The epitope specificity of CD4+ clone 9G8, recognizing both HIV-1(LAI) and HIV-1(MN) envelope, was within the 571-590 amino acid envelope region. Sequence analysis of the first infectious autologous strain revealed two amino acid mutations within this region. The 9G8 CTL clone induced by immunization failed to recognize targets expressing the corresponding CTL epitope from the infecting virus. Moreover, a peptide based on the epitope sequence of the infecting isolate antagonized the vaccine-induced CTL clone such that the CTL clone was no longer able to recognize the vaccine strain or HIV-1(MN) epitope. These findings suggest a potentially novel mechanism associated with vaccine failure whereby the infecting virus may not only escape from CTL activity, but also alter the ability of CTL to recognize other variants in an individual.