BACKGROUND: Number of studies has been performed to investigate the association of NAD (P) H quinine oxidoreductase 1 (NQO1) rs1800566 polymorphism with risk of bladder and prostate cancers, but presented inconsistent results. Therefore, we performed a meta-analysis to provide a comprehensive data on the association of NQO1 rs1800566 polymorphism with bladder and prostate cancers. METHODS: All eligible studies were identified in PubMed, Google Scholar, EMBASE, and China National Knowledge Infrastructure databases before June 01, 2019. RESULTS: A total of 22 case-control studies including 15 studies with 4,413 cases and 4,275 controls on bladder cancer and 7 studies with 762 cases and 1,813 controls on prostate cancer were selected. Overall, pooled data showed that the NQO1 rs1800566 polymorphism was significantly associated with an increased risk of bladder cancer (T vs. C: OR 1.300; 95% CI 1.112-1.518; P = 0.001; TT vs. CC: OR 1.415; 95% CI 1.084-1.847; P = 0.011; TC vs. CC: OR 1.389; 95% CI 1.111-1.738; P = 0.004; TT + TC vs. CC: OR 1.428; 95% CI 1.145-1.782; P = 0.002) and prostate cancer (TC vs. CC: OR 1.276; 95% CI 1.047-1.555; P = 0.016; TT + TC vs. CC: OR 1.268; 95% CI 1.050-1.532; P = 0.014). The stratified analysis by ethnicity revealed an increased risk of bladder cancer among Caucasians and prostate cancer among Asians. CONCLUSION: This meta-analysis suggested that the NQO1 rs1800566 polymorphism was significantly associated with increased risk of bladder and prostate cancers.