Cytotoxic T-lymphocytes (CTL) play an important role in the control of human immunodeficiency virus (HIV) and of human cytomegalovirus (HCMV) infection. Following highly active antiretroviral therapy (HAART), most studies have demonstrated a decline in the frequency of HIV-specific CTL. We analysed the effect of HAART on the size, phenotype and function of individual HIV- and HCMV-specific CTL clones, using clonotypic oligonucleotide probing specific for the T-cell receptor (TCR) β-chain hypervariable sequence of defined immunodominant CTL clones specific for peptides of HIV or HCMV, and quantified the limiting dilution analysis frequencies of CTL precursors (CTLp) specific for the same viral peptides. We found that the clonal composition of CD8+ T cells specific for HIV gag and env epitopes was highly focused and did not change after HAART. Following HAART, there was progressive contraction of HIV-specific CD8+ clones, especially in the CD28− CD27− subpopulation – the remaining cells of contracting HIV-specific clones were predominantly CD28− CD27+ CD45ROhi. We observed maintenance of strong functional HIV-specific CD8+ T-cell responses in limiting dilution analysis following HAART, indicating preferential loss of HIV-specific cells that have reduced cloning efficiency in vitro. Following HAART, we also observed selective expansion of HCMV-specific CD8+ clones. Most HCMV-specific CD8+ clones were predominantly CD28− CD27+/– CD45RAhi following HAART. In one subject, a Vβ6.4+ clone specific for HCMV pp65 selectively expanded following HAART, without expansion of two other Vβ6.4+ clones, indicating that individual clonotypes specific for the same peptide can show different kinetics and phenotypes in response to antiretroviral therapy.