HIV/AIDS and its treatment often alter body composition and result in poorer physical functioning. The aim of this study was to determine the effects of a moderate-intensity exercise program on body composition and the hormones and cytokines associated with adverse health outcomes. HIV-infected males (N = 111) were randomized to an exercise group (EX) who completed 6 weeks of moderate-intensity exercise training, or to a nonintervention control group (CON). In pre- and postintervention, body composition was estimated via DXA, peak strength was assessed, and resting blood samples were obtained. There was a decrease in salivary cortisol at wake (P = 0.025) in the EX and a trend (P = 0.07) for a decrease 1 hour after waking. The EX had a significant increase in lean tissue mass (LTM) (P < 0.001) following the intervention. Those in the EX below median body fat (20%) increased LTM (P = 0.014) only, while those above 20% decreased fat mass (P = 0.02), total fat (N = 0.009), and trunk fat (P = 0.001), while also increasing LTM (P = 0.027). Peak strength increased between 14% and 28% on all exercises in the EX group. These data indicate that 6 weeks of moderate-intensity exercise training can decrease salivary cortisol levels, improve physical performance, and improve body composition in HIV-infected men.