Immune reconstitution after antiretroviral therapy in human immunodeficiency virus (HIV)infected patients may result from the recovery of thymus function, peripheral redistribution, or decreased T cell destruction. This study investigated levels of T cell receptor gene rearrangement excision circles (TRECs) as a measure of recent thymic emigrant cells in peripheral blood lymphocytes of 50 HIV-infected infants and children who were followed-up for 40 months after the start or change of antiretroviral therapy. At baseline, patients exhibited fewer TRECs than did uninfected control subjects. The increase in TRECs after antiretroviral therapy was greater in infants than in older HIV-infected children. Of interest, patients who demonstrated discordant responses (i.e., increased CD4 T cell counts without significant virologic suppression) also had substantial gains in TRECs. Furthermore, TRECs correlated positively with the number of CD4 and naive T cells and negatively with age and virus load. Measurement of TRECs may serve as a useful tool for evaluating immune reconstitution in HIV-infected children receiving antiretroviral therapy.