ObjectiveThe aim of this study was to evaluate the effect of HIIT and SIT programmes on body composition, blood pressure, lipid profile, glucose, cardiorespiratory fitness, and strength of adolescents and to compare the effect between those different protocols.MethodsSixty adolescents were recruited from a high school and were randomly placed into three groups. SIT and HIIT undertook a training for 8 weeks, twice a week, for 12 min per session, during their Physical Education lessons. SIT group performed 6 sets of 60 s of work (90-95%HRmax) / 60 s of rest (50-55%HRmax), and HIIT group performed 3 sets of 2 min of work (80-85%HRmax) / 2 min of rest (50-55%HRmax).ResultsAfter adjustment by sex, both experimental groups exhibited a significant reduction in fat mass (p < 0.01), and trunk fat mass (p < 0.01), as well as a significant increase in lean mass (p = 0.01; <0.01), hand-grip strength (p < 0.01) and standing long jump (p = 0.05–0.04, respectively). In addition, HIIT showed a significant (p < 0.05) improvement in blood pressure, diastolic blood pressure, heart rate and VO2max, and a tendency toward a significant reduction in low density lipoprotein.ConclusionThe implementation of a HIIT protocol within high school Physical Education sessions, maintained for 8 weeks, at a rate of 3 sets of 2 min of work (80–85% RHR)/2 min of rest (50–55% RHR) generated adaptations such as improved fitness condition, changes in body composition, and improvements in blood parameters and blood pressure. However, the group of adolescents who performed SIT, shorter but more intense sets, did not experience as many benefits.