Because of lacking studies of urolithiasis in children, we detected the biochemical metabolic levels and FokⅠ polymorphisms in the vitamin D receptor (VDR) in Uyghur children with urolithiasis, and evaluated the associations of biochemical metabolic levels with FokⅠ genotypes. We included 142 Uyghur children (108 males) under age 14 years with a diagnosis of urolithiasis and 238 Uyghur children (154 males) under age 14 years without a history of urolithiasis as controls. Baseline information and data for serum and urine parameters were obtained from medical records. PCR-restriction fragment length polymorphism (PCR-RFLP) was used to analyze the VDR FokⅠ polymorphisms. In univariate analyses adjusting for age and sex, carbon dioxide combining power (CO2CP) (odds ratio [OR] = 1.13, 95% confidence interval [CI]: 1.07-1.19), serum magnesium (Mg) (OR = 1.27, 95% CI: 1.03-1.56) and serum chlorine (Cl) (OR = 0.93, 95% CI: 0.88-0.97) were related to Uyghur children urolithiasis risk. A multiple logistic regression model showed CO2CP (OR = 1.17, 95% CI: 1.09-1.26), levels of uric acid (OR = 1.01, 95% CI: 1.00-1.01) and serum sodium (Na) (OR = 0.90, 95% CI: 0.82-0.99) were associated with pediatric urolithiasis. The risk of urolithiasis was increased with the F versus f allele overall (OR = 1.42; 95% CI: 1.01-2.00) and for males (OR = 1.52, 95% CI: 1.02-2.27). However, metabolic levels did not differ by FokⅠ genotypes. In our population, CO2CP and levels of uric acid and serum Na as well as polymorphism of the F allele of the VDR FokⅠ may provide important clues to evaluate the risk of urolithiasis in Uyghur children.