We investigated the role of vitamin-D receptor gene (VDR) and calcitonin receptor (CTR) gene polymorphism in childhood nephrolithiasis in the north Indian population. A control group of 60 healthy paediatric individuals (age range 4-16 years) and 50 paediatric patients (age range 2-14 years) with kidney stones were examined. Polymorphism in both genes (VDR and CTR) was detected by using PCR-based restriction analysis. There was a statistically significant difference between the two groups for the genotypes of the VDR gene Fok-I polymorphism (P =0.007) and the CTR gene (P =0.048) polymorphism. The odds ratio (95% Confidence Interval) for the C allele in those at risk of stone disease was 1.83 (0.82-4.09) in VDR gene polymorphism and 1.99 (0.90-4.39) in the case of CTR gene polymorphism. Our results suggest that the effects of VDR (Fok-I) and CTR gene polymorphism contribute to the understanding of the pathogenesis of urinary calculi. It is also suggestive of a potential candidate gene in the search for genetic causes of paediatric calcium oxalate nephrolithiasis.