OBJECTIVE: To examine whether physical activity (PA) and sedentary time (ST) in primary school-aged children are associated with adiposity at the start of secondary school, and whether these associations differ by sex or ethnic group. DESIGN: Nationally representative prospective cohort study. SETTING: Children born across the UK, between 2000 and 2002. PARTICIPANTS: 6497 singleton children. OUTCOME MEASURES: Measures of adiposity (body mass index (BMI), fat mass index (FMI) and fat free mass index (FFMI))--obtained at 7 and 11 years. EXPLANATORY MEASURES: Total daily PA (mean counts per minute (cpm)); minutes of moderate-to-vigorous PA (MVPA); and ST. All assessed at 7 years using accelerometers. RESULTS: In cross-sectional analyses, total PA was inversely associated with FMI (3.7% (95% CI 2.7% to 4.7%) reduction per 150 cpm increase), as was MVPA (4.2% (CI 3.2% to 5.2%) reduction per 20 min/day increase). Associations were stronger in black and South Asian ethnic groups. Total PA and MVPA were not associated with FFMI. ST was positively associated with FMI (1.3% (CI 0.2% to 2.3%) increase per 50 min/day increase) and inversely associated with FFMI (0.5% (CI 0.2% to 0.7%) reduction per 50 min/day increase). Longitudinally, MVPA at age 7 years remained inversely associated with FMI at age 11 years (1.5% (CI 0.4% to 2.6%) reduction per 20 min/day increase). No association was found between total PA and ST and any of the later adiposity measures. CONCLUSIONS: 7-year-old children who are more physically active are less likely to be obese at that age and at age 11 years. These associations were particularly evident in children from black or South Asian ethnicity at age 7 years and in boys at age 11 years. Measurements of fat mass provide valuable insights into ethnic differences in associations between adiposity and activity.