Building on the success of combination antiretroviral drug therapy will require a better understanding of the underlying basis for viral persistence. Characterization of the therapeutic, viral, and immunological factors that influence the size and stability of viral reservoirs will foster the development of strategies to control or eliminate HIV-1 from infected individuals. Here we review recent work aimed at delineating the complex interplay between viral replication, the immune system, and viral reservoirs. Finally, we address the implications and clinical significance of the residual replication that persists in infected individuals on potent antiretroviral therapy to evaluate both the possible risks and benefits of ongoing HIV-1 replication.