We examined the associations between the physical, social, and policy environments of schools and adiposity in 9-10 year old children in Norfolk, UK. The relationships between 56 school-level variables and Fat Mass Index (FMI; fat mass (kg)/height (m2)) were investigated among 1724 well characterised children from 92 schools in this cross-sectional study. After stepwise removal of variables from multilevel linear regression models stratified by gender, only three variables were significantly associated with FMI. Among girls, attending a school with more pupils in the year group was associated with lower FMI, and attending a school with better cycle provision was associated with higher FMI. In boys being allowed to eat any food at break-time was associated with higher FMI. There was some evidence of moderation of the relationship between cycle provision and FMI by urban-rural location. These data suggest that few school factors are associated with FMI, and provide limited pointers to inform potential future school-based interventions to reduce obesity.