The role of the thymus in long-term immune reconstitution has not been addressed in HIV patients who were severely immunodeficient prior to successful treatment with combination antiretroviral therapy (ART). Adult HIV-1 patients (n = 78) with nadir CD4(+) T cell counts < 100 T cells/ mu l, at least 12 months on ART and 6 months of complete viral suppression (< 50 HIV RNA copies/ml) were selected from a patient database. The cohort was divided according to current CD4(+) T cell counts and patients from the lowest (n = 15) and highest (n = 12) tertiles were studied. Thymic volume was assessed by spiral computed tomography. Naive (CD45RA(+) CD62L(+)) and replicating (Ki67(+)) T cells were quantitated by flow cytometry, T cell receptor excision circles (TREC) were assessed by real-time PCR, and serum IL-7 and testosterone by immunoassay. Patients with low CD4(+) T cell counts had smaller thymuses [0(0 - 5.3) vs. 3.5(0 - 15.6) cm(3), p = 0.04] and were more likely to have no detectable thymus. They had similar proportions of replicating cells, but fewer naive CD4(+) and CD8(+) T cells and less TREC in CD4(+) and CD8(+) T cells/ml of blood than patients with high CD4(+) T cell counts. However, some patients with no detectable thymus had high numbers of naive and TREC-bearing T cells. Thus, the recovery of CD4(+) T cells in severely immunodeficient HIV patients with a virological response to ART is probably limited by thymic function. However, the data are consistent with extrathymic T cell production contributing to the naive T cell pool in some patients.