Our objective was to determine whether treatment-naive HIV-infected adolescents manifest abnormalities in thymus function and peripheral T cell repertoire, and to assess relationships of these immunologic characteristics with each other, with plasma HIV virus load, and T cell surface markers. TCR Vβ repertoire was determined by CDR3 length spectratyping in purified CD4+ and CD8+ T cells of high-risk, HIV-negative adolescents and of treatment-naive, HIV-infected adolescents. Thymus function was investigated by the simultaneous examination of T cell receptor excision circles (TRECs) in the CD4+ and CD8+ T cell subsets. HIV-infected adolescents exhibited significantly greater perturbations in their TCR Vβ repertoire in comparison with HIV-negative subjects. Perturbations in the CD8+ T cell compartment were more profound in comparison with CD4+ T cells. The CD4+ TCR Vβ perturbations were negatively correlated with the total and phenotypically naive CD4+ T cells, and with CD4+ TRECs. CD8+ TRECs, although not correlated with CD8+ TCR Vβ perturbations, showed negative correlation with memory and activated CD8+ T cells. Enterestingly, TRECs in CD4+ and CD8+ T cells were not significantly different between HIV-infected and uninfected adolescents. The TCR Vβ repertoire in adolescents is profoundly perturbed even in early stages of HIV infection, when total CD4+ cell counts in most subjects are within normal limits. The correlative analyses demonstrating negative association of CD4+ cell TRECs with CD4+ TCR Vβ perturbations and of CD8+ TRECs with CD8+ cell activation markers provide evidence of the intense activation of the central and peripheral immune compartments in this study population.