Human immunodeficiency virus (HIV)-specific CD8+ T cells play an important role in controlling HIV infection. Accurate monitoring of these cells is crucial in determining the effects of HIV therapy and vaccine efficacy. Using an intracellular cytokine staining based assay, we are able to directly quantify functional HIV-specific CD8+ T cells. This assay is highly reproducible, and can be performed using both fresh and cryopreserved peripheral blood cells. Importantly, this assay can be used to examine multiple HIV-peptide epitopes simultaneously, and is independent of patient HLA haplotype. Here, we examine the HIV-specific CD8+ T cell response to 95 optimized HIV-derived cytotoxic T lymphocyte (CTL) epitopes in 21 HIV-infected patients of varying HLA haplotype, using peptide mixes and matrices. We find that when using mixes of multiple HIV peptides, the CD8+ T cell response to the mixture is equivalent to the sum of the responses to the individual peptides contained therein. Detailed comparison of the responses in patients suggests that most patients generate a diverse CD8+ T cell response, recognizing multiple HIV epitopes derived from HIV Gag, Pol, Env, or Nef. Although some patients sharing HLA alleles occasionally recognize common peptides, rarely are responses to those peptides dominant within the same group of patients. These results confirm our previous findings that the responses to single HIV-peptides are rarely representative of the entire HIV response.