The reasons for poor CD4؉ T-cell recovery in some human immunodeficiency virus (HIV)-infected subjects despite effective highly active antiretroviral therapy (HAART) remain unclear. We recently reported that CXCR4-using (X4) HIV-1 could be gradually selected in cellular reservoirs during sustained HAART. Because of the differential expression of HIV-1 coreceptors CCR5 and CXCR4 on distinct T-cell subsets, the residual replication of R5 and X4 viruses could have different impacts on T-cell homeostasis during immune reconstitution on HAART. We examined this hypothesis and the mechanisms of CD4 ؉ T-cell restoration by comparing the virological and immunological features of 15 poor and 15 good immunological responders to HAART. We found a high frequency of X4 viruses in the poor immunological responders. But the levels of intrathymic proliferation of the two groups were similar regardless of whether they were infected by R5 or X4 virus. The frequency of recent thymic emigrants in the poor immunological responders was also similar to that found in the good immunological responders, despite their reduced numbers of naïve CD4 ؉ T cells. Our data, rather, suggest that the naïve T-cell compartment is drained by a high rate of mature naïve cell loss in the periphery due to bystander apoptosis or activation-induced differentiation. X4 viruses could play a role in the depletion of naïve T cells in poor immunological responders to HAART by triggering persistent T-cell activation and bystander apoptosis via gp120-CXCR4 interactions.Highly active antiretroviral therapy (HAART) successfully controls human immunodeficiency virus type 1 (HIV-1) replication in most individuals, resulting in substantial immune restoration and decreased morbidity and mortality. However, the suppression of detectable HIV-1 viremia does not invariably result in a significant increase in CD4 ϩ T cells. Five to 15% of HIV-infected patients still have a CD4ϩ T-cell counts of Ͻ200 cells/l and are thus at risk of developing AIDS, despite being on HAART for several years (15, 23).The mechanisms responsible for these persistently low CD4 ϩ T-cell counts are not clear; they could be due to impaired reconstitution or to excessive destruction of CD4 ϩ T cells. The recovery of peripheral CD4 ϩ T-cell counts in patients on HAART depends mainly on a slow increase in naïve CD4 ϩ T cells (3). Several studies have suggested that the thymus plays a role in immune reconstitution during HIV-1 infection, even in adults (12,34,36), but the extent to which it determines the regeneration of the peripheral CD4 ϩ T-cell pool in patients on HAART remains unclear. Analyses of thymic activity are hampered by the difficulty of directly measuring thymic output. Most studies have measured the signaljoint (sj) T-cell receptor (TCR) excision circle (TREC) in blood T cells. This surrogate marker of thymic activity is a byproduct of the TCR␦ locus rearrangement within the TCR␣ locus (␦Rec-J␣ rearrangement) that occurs during thymopoiesis (5,11,12,36,44). However, TRECs persist in recen...