HIV infection decreases thymic output and induces chronic T-cell activation.To examine the reconstitution of naive and activated T cells.Extended immune phenotyping of CD4 + and CD8 + T-cell subsets was combined with T-cell receptor rearrangement excision circle (TREC) levels and measures of T-cell receptor repertoire perturbations in CD8 + T-cell subpopulation to define the global effect of HIV-1 on T-cell dynamics. Evaluations before and after therapy were performed in HIV-infected children and compared with those in healthy individuals.Ten HIV-infected children and adolescents with a broad range of pretherapy CD4 + T-cell counts were compared with healthy individuals. Pretherapy late activated CD8 + T cells (CD3 + CD8 + CD45RA + CD27 − CD11a bright cells) were expanded among HIV-infected subjects. Successful antiretroviral therapy increased the proportion of naive T cells (CD3 + CD4 + CD45RA + CD27 + CD28 + and CD3 + CD8 + CD45RA + CD27 + CD11a dim cells), with a significant decrease in late activated CD8 + T cells. The proportion of naive CD4 + and CD8 + T cells significantly predicted log 10 TREC copies/10 6 PBMCs in infected children and healthy control subjects, with a negative correlation in late activated CD8 + T cells and activated CD4 + T cells. Treatment re-established Gaussian distributions and decreased oligoclonal expansion within the Vβ repertoire of CD8 + CD45RA + T cells, but compared with that seen in healthy children, the proportion of late activated CD8 + T cells remained increased.HIV infection strikingly shifts the proportion of naive and late activated CD45RA + CD8 + T cells. Homeostasis within this T-cell population reflects TREC levels and the extent of T-cell receptor Vβ perturbations.