The nef gene is conserved among primate lentiviruses and is one of the first viral genes that is transcribed following infection. This suggests a critical role for Nef in the virus life cycle and in the pathogenesis of lentiviral infections. In vitro, several functions have been described, including down regulation of CD4 and MHC class I surface expression, altered T-cell signaling and activation, and enhanced viral infectivity. However, the impact of these individual functions on viral pathogenicity in general, and thymic T cell production in particular, remains elusive. Here, we review the observations from experimental models that have been used to study the pathogenic effect of HIV-1 Nef on the thymus. These in vitro and in vivo studies have led to a better understanding of Nefs mechanism of action, although there still exists discord as to the contribution of Nef-mediated disturbance of thymopoiesis in the pathogenesis of AIDS.