The present study was undertaken to determine whether children with lower bone mass display lower muscle mass for their height than those with high bone mineral content (BMC) and whether appendicular lean mass (bone-free lean mass in arms plus legs) is associated with physical activity and/or BMC in preschool children. 158 children (59% male) from a New Zealand cohort born in 2001-2002 were studied close to their fifth birthday. Body composition was measured by dual energy X-ray absorptiometry (Lunar DPX-L). Lean mass index (LMI) was calculated as lean mass (kg) divided by height in metres squared. Physical activity was assessed objectively by accelerometry (Actical Mini-Mitter). Girls and boys had similar heights, weights and daily accelerometry counts but boys had lower fat mass, and higher lean mass and total body BMC than the girls (P<0.00l). In both sexes children with greater quantities of total and regional lean mass and higher LMI values had significantly higher bone mass. Appendicular LMI was more strongly associated with BMC than LMI. Accelerometry counts showed no associations with height but were positively associated with lean mass (r=0.23, P<0.03), appendicular LMI (r=0.25 P<0.01), total body BMC (r=0.24, P<0.02) and total body less head BMC (r=0.27 P<0.009) in the boys, but not in the girls. Greater time spent in more intense physical activity was also associated with higher appendicular lean mass and TBLH BMC only in the boys. We conclude that children with lower BMC values display not only lower lean mass but also lower total and appendicular lean mass for their height, than those with higher BMC values. The sex differences in associations of accelerometry counts to lean mass and BMC have been noted by others and require further investigation.