OBJECTIVE: Evidence suggests that area-level deprivation is associated with obesity independently of individual socioeconomic status; however, although the school may also have an impact on child health, few studies have investigated the association between school-level deprivation and the body mass index (BMI) of students. The aim of this study was to assess the relationship between the BMI for children of different ages and area-level and school-level deprivation. SUBJECTS: BMI measurements were collected through the National Child Measurement Programme (NCMP) that samples from two school years: 396,171 reception year pupils (4-5-year olds) and 392,344 year 6 pupils (10-11-year olds) from 14,054 primary schools in England. DESIGN: Cross-classified multilevel models with four levels: individual (n=788,525), lower super output areas corresponding to area of residence (n=29,606), schools (n=14,054) and primary care trusts (PCTs, n=143), which coordinate the collection of data within a large area, were used to study the relationship between measures of deprivation at an area and school level, and childhood BMI within England. RESULTS: A positive association was found between the area and school measures of deprivation, and student BMI. Both the measures of deprivation explained a greater proportion of variance in BMI z-scores for year 6 students than for the reception year students, with a greater difference between the year groups found with the school-level measure of socioeconomic status than for the the area-level measure. CONCLUSIONS: Deprivation explains a greater proportion of the variance in BMI for older compared with younger children, perhaps reflecting the impact of deprivation as children age, highlighting the widening of health inequalities through childhood. The association with school-level deprivation illustrates the impact of the school on BMI status throughout the primary school years.