The aim of this study was to verify the relationship between habitual physical activity and body fat in HIV/AIDS subjects on highly active antiretroviral therapy. This was a cross-sectional study covering 169 men and 51 women. It was conducted at the AIDS Clinic of the School of Medicine, University of São Paulo. The dependent variables analysed were central subcutaneous fat (CSF) and waist-to-hip-ratio (WHR). The independent variable was the score for leisure time physical activity (LTPA). The control variables were sex, age, education, energy intake, body mass index, smoking, diagnosis of AIDS, T-CD4+ lymphocyte levels and duration of use of protease inhibitors. Multiple linear regressions were used for statistical analysis. After controls, there was significant negative correlation for LTPA with CSF (beta=-2.849; Pvariable=0.013; r2(adjusted)=0.65; Pmodel<0.001), and LTPA was in the limit of the significance with WHR (beta=-0.005; Pvariable=0.073; r2(adjusted)=0.41; Pmodel<0.001). Physical activity contributed towards preventing fat accumulation in HIV/AIDS subjects.