Vitamin D is associated with a wide range of other functions beyond bone development. We evaluated the factors associated with 25-hydroxyvitamin D levels in 974 children aged <= 10 years and the impact of BsmI polymorphism of the vitamin D receptor (VDR) gene (rs1544410) on metabolic parameters in a subsample (n: 430) with a follow-up 2 years later from the initial population-based cross-sectional study. Multiple linear regression models were used in the analyses. The prevalence (95% CI) of vitamin D deficiency, insufficiency and sufficiency of children was 11.1% (9.2-13.2), 21.8% (19.2-24.5) and 67.2% (64.1-70.1), respectively. Overall, 23% of the variation in serum 25-hydroxyvitamin D concentrations was accounted for by BsmI polymorphism beta = -0.053 (95% CI) (-0.100, -0.006), maternal schooling (>= 9 years) beta = 0.100 (0.039, 0.161), serum vitamin E beta = 0.478 (0.381, 0.574), total cholesterol concentration beta = 0.232 (0.072, 0.393) and serum folate beta = 0.064 (0.013, 0.115). BsmI polymorphism was positively associated with HOMA-IR beta = 0.122 (0.002, 0.243) and fasting glucose concentration beta = 1.696 (0.259, 3.133). In conclusion, variables related to socioeconomic level, the presence of the allele risk for BsmI and other nutrient concentrations were associated with serum 25-hydroxyvitamin D concentrations. Our results suggest that BsmI polymorphism is correlated with metabolic outcomes.