Studies of determinants of bone mineralization during growth are relevant to the attempt to increase peak bone mass. The aim of this study was to examine how calcium intake and physical activity influence bone size (bone area, BA), accretion in BA, whole body bone mineral content (BMC) and accretion in BMC. BA and BMC were examined by dual-energy X-ray absorptiometry (Hologic 1000/W) in healthy girls (n = 192) and boys (n = 140) aged 5-19 years at baseline and 1 year later. Calcium intake was assessed three times by a food frequency questionnaire and physical activity three times by a 24 h recall questionnaire. The influence of calcium intake and physical activity was examined by multiple regression. BA was size-adjusted by including height and weight in all analyses, and BMC was size-adjusted by including BA, height and weight in all analyses. Size-adjusted average BA was associated neither with average calcium intake nor with average physical activity. Size-adjusted accretion in BA was borderline associated with the average calcium intake in boys only (p = 0.07). Size-adjusted average BMC was positively associated with average calcium intake (p) = 0.03 girls; p = 0.07 boys) and borderline associated with average physical activity level in boys (p = 0.07) but not girls (p = 0.7). Size-adjusted accretion in BMC was significantly associated neither with average calcium intake nor with average physical activity level, but was associated with change in calcium intake over the 1 year observation period in boys (p = 0.03) but not girls (p = 0.9). In conclusion, we found that size-adjusted BMC in school-aged children was positively associated with average calcium intake. Size-adjusted accretion in BMC was positively associated with change in dietary calcium intake in boys only. To what degree this is caused by a reduction in remodeling space is unknown.