Recent studies show in patients with prolonged suppression of plasma virus by highly active antiretroviral therapy (HAART) that HIV-1 persists latently in resting CD4+ T lymphocytes, which may, at least in part, result from on-going viral replication in vivo. It is unclear where and how the viral replication occurred. We present here the replication and genetic characteristics of HIV-1 in the peripheral blood activated CD4+ T lymphocytes, resting CD4+ T lymphocytes and monocytes from twelve acutely infected patients who have been on HAART for up to 4 years. HIV-1 proviruses persisted in the activated CD4+ T lymphocytes and monocytes-macrophages as well as resting CD4+ lymphocytes. The levels of HIV-1 DNA in monocytes were lower than that in both activated and resting CD4+ T cells during the period of studied. There was no significant difference in HIV-1 DNA levels between resting CD4+ T cells and activated CD4+ T cells. However, the levels of HIV-1 unspliced mRNA, gag, and multispliced mRNA, tat, were significantly higher in activate CD4+ T cells and monocytes than that in resting CD4+ T cells. In two out of seven patients, more HIV-1 sequence variation was observed in activated CD4+ T cells and monocytes compared to that in resting CD4+ T cells. The later variants that resulted from continued HIV-1 replication were most closely associated with the early variants in monocytes and activated CD4+ T cells. These findings suggest in patients with undetectable plasma virus due to HAART that HIV-1 produced in monocytes and activated CD4+ T cells seed HIV-1 latent reservoirs in the blood.