The aim of this study was to determine and compare thymic output during 12 months of highly active antiretroviral therapy (HAART) in HIV-infected patients with different types of immune recovery. In total, 18 Thai HIV-infected patients with normal immune recovery (NR) and 13 Thai HIV-infected patients with slow immune recovery (SR) were enrolled. T-cell receptor rearrangement excision circle (TREC) levels in peripheral blood mononuclear cells (PBMCs) and CD4(+) T cells were quantified at baseline, and after 6 and 12 months of HAART. CD4(+) T-cell counts in NR patients were significantly higher than those in SR patients after 6 and 12 months of HAART. However, the median TREC levels in PBMCs and CD4(+) T cells in both groups were comparable. Moreover, TREC levels showed similar trends in PBMCs and CD4(+) T cells in both groups during 12 months of HAART. Only patients with SR had significant increases in median TREC levels in PBMCs and CD4(+) T-cells during the first 6 months of HAART. No correlations were found between CD4(+) T-cell count and TREC levels in PBMCs and CD4(+) T cells. These results imply that the increase in CD4(+) T-cell count in SR patients after 12 months of HAART is likely attributable to thymic output and other sources.