Objective: To understand the mechanisms underlying the differential targeting of T-cell responses during HIV-1 disease progression. Design: We performed a cross-sectional analysis of HIV specific CD8 T-cell responses in peripheral blood mononuclear cells (PBMC) obtained from 21 subjects with well characterized acute or early infection and 88 subjects with chronic HIV-1 infection. We also performed a longitudinal analysis of T-cell responses in five early infected subjects one of whom was studied extensively over a 4-year-period. Methods: PBMC were stimulated with pools of peptides encompassing all of the HIV-1 proteins in an interferon-γ ELISpot assay. A mean entropy score was calculated for each peptide in the HIV-1 genome. Results: The early infected group preferentially targeted variable peptides with higher entropy while responses towards more conserved peptides with lower entropy pre-dominated in the group with chronic infection. In five early infected subjects followed longitudinally, responses to variable proteins declined while those to conserved proteins increased over time. In the subject who was followed for 4 years, epitopes in Vif and Nef were targeted early and escape occurred in three of these four epitopes. During the chronic phase of his infection, the early responses waned with an associated increase in breadth of T-cell responses mainly to Gag and Pol epitopes. Conclusion: Taken together, these data demonstrate that HIV-specific CD8 T cells are directed preferentially to the variable peptides in early infection but diminish in frequency during chronic disease, in large part due to cytotoxic T lymphocyte escape. © 2005 Lippincott Williams & Wilkins.