The main aims of this study were, to evaluate what effect a change in fat mass (FM) and lean body mass (LBM) has on bone parameters over 2 years' time, in 7-year-old school children and to see what effect fitness had on bone parameters in these children. A repeated-measures design study was conducted where children born in 1999 from six elementary schools in Reykjavik, Iceland were measured twice. All children attending second grade in these six schools were invited to participate. Three hundred twenty-one children were invited, 211 underwent dual-energy X-ray absorptiometry (DXA) scans at the age of seven, and 164 (78 %) of the 211 had DXA scans again 2 years later. Increase in both FM and LBM was associated with increased total body bone mineral content (BMC) and bone area (BA). An increase in FM was more strongly positively associated with BA while an increase in LBM was more strongly associated with an increase in BMC. An increase in FM was negatively associated with change in bone mineral density (BMD), but an increase in LBM was positively associated with change in BMD. Fitness was positively associated with bone parameters when weight, height and sex were accounted for. The present results suggest that an increase in fat mass over 2 years is associated with an increase in BA and BMC, but a decrease in BMD in the whole body. An increase in LBM accrual, on the other hand, is positively associated with all bone parameters in the body. Fitness is associated with both BMC and BMD but not BA.