Background: Growing evidence has indicated that insulin-like growth factor binding protein-3 (IGFBP-3) polymorphisms are associated with altered risk of prostate cancer (PCa). However, few studies have been conducted in Chinese population to validate this association. Materials and methods: Herein, we examined the association between genetic variants in the IGFBP-3 gene and PCa risk in the Chinese Han population based on a genome-wide association study (1,417 cases and 1,008 controls), and replicated three genetic variants loci in an independent case-control study (1,755 cases and 1,523 controls) using Sequenom platform. Logistic regression analyses were performed to estimate odds ratios (ORs) and 95% confidence intervals (95% CIs). Results: We found that in the discovery stage, rs9691259 (OR=0.691, 95% CI: 0.587-0.814, P<0.001) and rs6950179 (OR=1.420, 95% CI: 1.201-1.677, P<0.001) were significantly associated with PCa risk, whereas rs2854744 showed a marginal association with PCa risk. In the replication stage, the association between rs9691259 and rs6950179 and PCa risk was not replicated, whereas rs2854744 conferred a significant association with PCa risk (OR=1.399, 95% CI: 1.010-1.937, P=0.043). After combining the two stages, we found that rs9691259, rs6950179, and rs2854744 were all significantly associated with PCa risk. Conclusion: This study suggests that IGFBP-3 genetic variants are significantly associated with PCa risk in the Chinese population.