The purpose of this study was to examine youth physical activity (PA) in free-time periods during high school days and their contribution to total PA. Differences in terms of sex, age, body mass index and school level were assessed in a sample of Portuguese adolescents. Participants totalled 213 (135 girls), aged 14.6 ± 1.7, from two different Portuguese schools, 69 attending an urban school and 144 attending a rural school. Activity levels of five free-time periods were assessed with an accelerometry-based activity monitor (ActiGraph). The results indicated that boys had significantly higher levels of PA (counts min[superscript-1]) than girls for two of the five periods (afternoon recess and after-school time). Activity levels were higher among younger students during three periods (before school, morning recess and afternoon recess). Significant differences in activity levels (p < 0.001) between the two schools were also found. Despite being older the rural students were more active than urban. In conclusion, free-time periods in high school are a relevant context for PA promotion. In this study they contributed significantly for total daily PA in both sexes, with 37.7-42.7% for girls and 40.1-42.1% for boys.