There are two models for CD4+ T-cell depletion leading to AIDS: a kinetic model and an immune suppression model. In the kinetic model, direct cell killing due to viral replication results in a continuous demand for CD4+ T-cells, which eventually exhausts their capacity for renewal by proliferative mechanisms. In the immune suppression model, CD4+ T-cell decline is due to an indirect global inhibitory effect of the virus on uninfected immune cell function. In order to address differences in the two models, we investigated proliferative history and thymic output in PBMC from the GRIV cohort of fast (FP) and slow/non-progressors (S/NP), and uninfected controls. Proliferative history and thymic output were assessed by measurement of mean telomeric restriction fragment (TRF) length and T-cell receptor Rearrangement Excision Circles (TREC) levels, respectively. Mean TRF lengths were significantly shorter in S/NP (n = 93, 7.59 ±0.11 kb) and FP (n = 42, 7.25 ± 0.15 kb) compared to controls (n = 35, 9.17 ± 0.19 kb). Mean TRF length in PBMC (n = 9, 7.32 ± 0.31 kb) and CD4+ enriched fractions (n = 9, 7.41 ± 0.30 kb) from a subset of non-GRIV HIV-1 infected samples were also significantly smaller than PBMC (n = 8, 9.77 ± 0.33 kb) and CD4+ fractions (n = 8, 9.41 ± 0.32 kb) from uninfected controls. Rates of telomeric shortening, however, were similar among S/NP (n = 93, −45 ± 20 bp/yr), FP (n = 42, −41 ± 14 bp/yr) and controls (−29 ± 17 bp/yr). Paralleling differences observed in mean TRF length, TREC levels were significantly reduced in S/NP (n = 10, 3,433 ± 843 mol/μ and FP (n = 8, 1,193 ± 413) compared to controls (n = 15, 22,706 ± 5,089), indicative of a defect in thymopoiesis in HIV-1 infection. When evaluated in the context of reduced thymopoiesis, the difference in mean TRF length between S/NP and controls (1.58 ± 0.30 kb) is similar to that observed between memory and naïve T-cells (1.4 ± 0.1 kb), and may reflect perturbations in the peripheral T-cell population due to a decline in thymic output of naïve T-cells rather than increased turnover. Based on the different clinical criteria used to select S/NP and FP, the slight difference in TREC between these two groups suggests the threshold for pathogenesis as a result of naïve T-cell depletion may be quite low, and incremental increases in thymic output may yield substantial clinical results. Future studies regarding therapeutic vaccination, specifically with HIV-1 Tat targeted anti-immunosuppressive vaccines, should address the defect in thymic output in HIV-1 infection by using TREC analysis as a rapid method for biological evaluation.