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Background  There is increasing policy interest in ensuring that the school environment supports healthy behaviours. We examined the cross-sectional and longitudinal associations between schools’ policies, programmes and facilities for physical activity (PA) and adolescents’ objectively-measured activity intensity during the school day and lunchtime.    Methods  Accelerometer-derived PA (proportion of time spent in sedentary (SED), light PA (LPA) and moderate-to-vigorous PA (MVPA)) during school hours and lunchtime from 325 participants in the SPEEDY study were obtained from baseline measurements (primary school, age 9/10 years) and +4y follow-up (secondary school). School environment characteristics were assessed by teacher questionnaire. Multivariable multi-level linear regression analyses accounting for school and adjusted for sex, age, BMI and family socio-economic status assessed cross-sectional associations with lunchtime and school-day SED, LPA and MVPA; effect modification by sex was investigated. The association of changes in school environment with changes in outcomes was examined using multivariable cross-classified linear regression models.    Results  There were significant differences between primary and secondary schools for 6/10 school environment characteristics investigated (including secondary schools reporting shorter breaks, more lunchtime PA opportunities, and higher number of sports facilities). Cross-sectional analyses showed that boys attending secondary schools with longer breaks spent significantly less time in SED and more time in MVPA during the school day. Longitudinally, an increase in break-time duration between primary and secondary school was associated with smaller reductions in MVPA during the school day. Moreover, participants who moved from a primary school that did not provide opportunities for PA at lunchtime to a secondary school that did provide such opportunities exhibited smaller increases in SED and smaller reductions in MVPA at lunchtime.    Conclusions  Schools should consider the potential negative impact of reducing break time duration on students’ MVPA and SED during the school day. School-based interventions that combine longer breaks and more PA opportunities during lunchtime may be a fruitful direction for future research. Further research should also explore other factors in the school environment to explain the school-level clustering observed, and study sex differences in the way that the school environment influences activity intensity for adolescent populations.    Electronic supplementary material  The online version of this article (doi:10.1186/s12966-016-0378-6) contains supplementary material, which is available to authorized users.

the international journal of behavioural nutrition and physical activity

School polices, programmes and facilities, and objectively measured sedentary time, LPA and MVPA: associations in secondary school and over the transition from primary to secondary school