The aim of this study was to evaluate the impact on muscle strength, aerobic fitness and body composition, of replacing the physical education (PE) class of Colombian adolescents with resistance or aerobic training. 120 tanner stage 3 adolescents attending a state school were randomized to resistance training, aerobic training, or a control group who continued to attend a weekly 2- hour PE class for 16 weeks. The resistance training and aerobic training groups participated in twice weekly supervised after-school exercise sessions of 1 hour instead of their PE class. Sum of skinfolds, lean body mass (bioelectrical impedance analysis), muscular strength (6 repetition maximum (RM)) bench press, lateral pulldown and leg press) and estimated cardiorespiratory fitness (multistage 20 meter shuttle run) were ssessed at pre and post intervention. Complete data were available for n = 40 of the resistance training group, n = 40 of the aerobic training group and n = 30 PE (controls). Resistance raining attenuated increases in sum of skinfolds compared with controls (d = 0.27, [0.09–0.36]). We found no significant effect on lean body mass. Resistance training produced a positive effect on muscle strength compared with both controls (d = 0.66 [.49-.86]) and aerobic training (d = 0.55[0.28–0.67]). There was a positive effect of resistance training on cardiorespiratory fitness compared with controls (d = 0.04 [-0.10–0.12]) but not compared with aerobic training (d = 0.24 [0.10–0.36]). Replacing a 2-hour PE class with two 1 hour resistance training sessions attenuated gains in subcutaneous adiposity, and enhanced muscle strength and aerobic fitness development in Colombian youth, based on a median attendance of approximately 1 session a week. Further research to assess whether adequate stimuli for the development of muscular fitness exists within current physical education provision is warranted.