To investigate the effect of the vitamin D receptor (VDR) Fok I Bsm I Dde I Apa I Taq I polymorphism on the clinical presentation of calcium urolithiasis, 464 patients with urolithiasis and 450 age- and sex-matched healthy controls were recruited from The First Affiliated Hospital of Zhejiang University between January 2010 and March 2011. Five SNPs of VDR polymorphism were detected using polymerase chain reaction-based restriction analysis. The frequency of VDR Apa I genotypes between the patients and the healthy controls was significantly different (P = 0.006). Apa I a allele was found to be associated with increased risk of stone recurrence (P = 0.028). We also found Fok I Dde I Apa I showed a significant difference between male and female in the patients group (P < 0.05). Haplotype analysis of the five VDR polymorphisms showed a significant association with urolithiasis (global-P value = 0.0001). Genetic polymorphisms of VDR are important in the clinical presentation of patients with calcium urolithiasis in the Han population of southern China.