Upon the initiation of highly active antiretroviral therapy (HAART) for the treatment of HIV infection, the level of viral RNA in the blood rapidly decays in at least two distinct phases (12, 28), according to the death rates of cells that were already infected before treatment began. First-phase decay occurs during the first 7 to 10 days of treatment and has a half-life of 0.9 to 1.6 days (6,28,29), reflecting the death rate of productively infected CD4 ϩ T cells. The slower second phase occurs over a period of weeks and exhibits a half-life of approximately 14 days (28), corresponding to the turnover rate of long-lived infected cells. Second-phase sources of virus are believed to include cells of the monocyte/macrophage lineage and may also include infected resting CD4 ϩ T cells carrying unintegrated DNA (preintegration latent cells), follicular dendritic cells harboring intact virions, infected CD4 ϩ T cells that are not cleared by the host immune response, and an as-yet-unidentified cell type (4,12,17,28,30). An extremely slow third phase of decay is detectable by more sensitive assays and has a half-life estimated to range from months to years (7, 11). The viremia in this phase is believed to result from the reactivation of latently infected CD4 ϩ T cells (11, 40) or low-level ongoing replication (8, 14, 32), or both (35).Recent clinical trials with the first clinically approved HIV-1 integrase (IN) inhibitor, raltegravir (RAL), have yielded promising results. The phase II Merck protocol 004 part II trial (22, 23) and the phase III STARTMRK trial (20) compared the activity of RAL to that of the nonnucleoside reverse transcriptase inhibitor (NNRTI) efavirenz (EFV), each as part of standard combination therapy in drug-naïve HIV-1-infected individuals. While both drugs showed equal efficacy for the long-term suppression of the viral load, the limit of detection was reached more rapidly with RAL. This has been attributed to levels of virus production from second-phase sources that were 70% lower with RAL-based treatment than with EFV-based treatment (26).Several hypotheses may explain these unique viral load decay dynamics. They include differences in the time until drug bioavailability, differences in drug potency, a role for cells latently infected preintegration, the greater penetration of certain drugs into sanctuary sites, the stage of viral replication targeted, and the IN inhibitor-induced accumulation of unintegrated viral DNA (15,23,26,33,34). On the basis of the mathematical modeling of viral load decay, it has been proposed that the clinical observations can be explained by the effect of RAL on cells latently infected preintegration (26). These models also suggest that differences in drug potency might play a minor role but are inconsistent with a role for sanctuary sites (26). The mathematical models of viral load decay prepared by others suggest that the stage of viral replication targeted by RAL versus that targeted by EFV can explain the clinical trial results but are inconsistent with roles for ...