Studies of lymphoid tissue from HIV-infected individuals have provided critical insights into the pathogenesis of HIV disease. Systemic dissemination of virus via the lymphatic system occurs at a very early stage after infection. Explosive viral replication within lymphoid tissue ensues, before the development of cell-mediated and humoral immune responses. By the time potent immune responses downregulate viral expression, an immense viral reservoir within lymphoid tissue has already been established. During the stage of dichotomy in viral load between lymph node and peripheral blood, the viral reservoir is maintained by the ability of the follicular dendritic cells (FDC) network to efficiently trap extracellular virions, as well as by immunologic and microenvironmental factors favoring infection of susceptible cells and sequestration of cells already infected. Degeneration of the FDC network and wholesale disruption of lymphoid architecture herald late-stage disease. The dysfunctional lymphoid tissue contributes directly to immunodeficiency and to sharp increases in viral burden and replication as mechanical and immune controls are lost. Studies in HIV-infected long-term nonprogressors indicate that these individuals are able to maintain cell-mediated and humoral immune responses against HIV. These immune responses are responsible, at least in part, for the maintenance of intact lymphoid tissue architecture and the low levels of viral burden and replication detected in these individuals. Studies of the effect of antiretroviral therapy on HIV infection in lymphoid tissue show that decreases in plasma viremia are associated with and most likely are caused by decreases in viral replication within lymphoid tissue. Further understanding of the pathogenic mechanisms within lymphoid tissue will have important implications for early intervention aimed at inducing a long-term nonprogressor state (i.e., preventing disruption of lymphoid tissue integrity), and later intervention aimed at arresting or even reversing damage to the lymphoid system.