Human immunodeficiency virus (HIV) infection is associated with progressive loss of circulating CD4⁺ lymphocytes. Treatment with highly active antiretroviral therapy (HAART) has led to increases in CD4⁺ T lymphocytes of naive (CD45RA⁺62L⁺) and memory (CD45R0⁺RA⁻) phenotypes. Thymic computerized tomography scans were obtained on 30 individuals with HIV disease to investigate the role of the thymus in cellular restoration after 48 weeks of HAART. Individuals with abundant thymic tissue had higher naive CD4⁺ T lymphocyte counts at weeks 2–24 after therapy than individuals with minimal thymic tissue. Individuals with abundant thymic tissue had significantly larger increases in naive CD4⁺ cells during the first 4 weeks of therapy. These individuals were also more likely to experience viral rebound despite comparable initial declines in plasma HIV-1 RNA. These findings suggest that there is a complex relationship among the thymus, viral replication, and lymphocyte restoration after application of HAART in HIV disease.