Dysregulation of both the cell cycle within the CD4(+) T cells and T cell responses is characteristic for pathogenic HIV infection in humans and experimental SIV infection in rhesus macaques. However, SIV infection in sooty mangabeys does not lead to either an AIDS-like disease or such CD4(+) T cell dysregulation. A previous study has highlighted a potential role for cell cycle regulatory proteins in these distinct clinical outcomes. This study was performed to characterize the effect of SIV infection on the expression of cell cycle-related molecules in CD4(+) T cells of rhesus macaques and sooty mangabeys in attempts to define activation-induced gene expression patterns associated with disease resistance or susceptibility. First, T cell receptor (TCR)-mediated cell activation induced gene expression profiles that were unique to CD4(+) T cells from SIV-naive sooty mangabeys and rhesus macaques. More importantly, distinct and reproducible gene expression patterns were detected in CD4(+) T cells as a result of in vivo SIV infection in animals from each of the two species. In addition, SIV infection in both species showed significant differential effects on TCR activation-induced expression with a reproducible alteration of 10 genes highlighted by discordant effects on expression of Cyclin D3, Cyclin B, and RAD17. Therefore SIV infection in rhesus macaques and sooty mangabeys exhibits distinct and reproducible effects on cell cycle regulation in CD4(+) T cells during T cell activation that may be the basis for disease susceptibility vs. resistance in these two species, respectively.