HIV infection and subsequent antiretroviral therapy have been associated with an increased incidence of dyslipidemia and cardiovascular disease and has been shown to suppress cholesterol efflux from virus-infected macrophages by inducing Nef-dependent downregulation of ABCA1. The SIV/macaque model was used to examine consequences and mechanisms involved. SIV infection drove a significant remodeling of high-density lipoprotein profiles suggesting systemic inhibition of the ABCA1-dependent reverse cholesterol transport pathway. The ABCA1 cholesterol transporter was significantly down regulated in the livers of the SIV-infected macaques and the viral protein Nef could be detected in the liver as well as in plasma of infected animals. Extracellular myristoylated HIV Nef inhibited cholesterol efflux from macrophages and hepatocytes. Moreover, sera from SIV-infected macaques also suppressed cholesterol efflux in a Nef-dependent fashion. These results indicate that SIV infection is a significant contributor to primary dyslipidemia, likely through the ability of Nef to suppress ABCA1-dependent reverse cholesterol transport.