The purpose of the present study was to examine the effects of 12-week exercise interventions on physical self-perceptions of male university students. The study also aimed to investigate the relationships between the changes in physical self-perceptions and the changes in some physiological measures after 12-week exercise programs. Forty-eight male university students aged from 19 to 25 years were enrolled in this study. Participants were randomly and equally assigned to swimming, running, cycling and control conditions. The Physical Self-Perception Profile was administered to all participants before and after 12-week exercise programs. Additionally, strength, maximal oxygen uptake (VO2max) and body compositions were assessed before and after interventions. Participants in the exercise groups attended swimming, running or cycling sessions for 40 min per day, 3 days per week with 60-70% of their heart rate reserves, while those in the control group did not attend any regular physical activity. The results of 4 x 2 x 5 MANOVA with the dimensions of physical self-perceptions as within-subject factor revealed that all groups including the control group revealed better physical-self-perceptions from pre- to post-test. Results of 4 x 2 x 3 MANOVA with physiological measures as within-subject factor revealed that VO2max values of participants in the swimming group improved more than the other groups. On the other hand, no significant differences were observed in strength scores and body fat levels among groups. Furthermore, no significant associations were obtained between the changes in physical self-perception dimensions and the physiological measures.