Background: NAD(P)H-quinone oxidoreductase 1 (NQO1) is a part of the antioxidant defense system. NQO1 protects cells from oxidative stress by maintaining antioxidant forms of ubiquinone and vitamin E and this enzymatic activity can be sufficient to protect against carcinogenesis. Oxidative stress may contribute to carcinogenesis as an important risk factor. This study aimed to investigate the relationship between prostate cancer and NQO1 C609T polymorphism in a Turkish population. Patients and Methods: Forty-five patients with prostate cancer and fifty healthy controls were included in this study. Gene polymorphism was determined by a restricted fragment length polymorphism-polymerase chain reaction (PCR-RFLP) method. Results: The NQO1 TT genotype was demonstrated to be increased inpatients, there were no significant differences between distributions of NQO1 C609T genotypes in the study groups. Serum PSA and alkaline phosphatase levels were elevated in patients carrying T alleles (TT > CT > CC). There were no correlations between tumor size, node classification, metastasis or stage and NQO1 genotypes. Conclusion: The results of our study of Turkish prostate cancer patients suggests that mutation of the NQO1 gene may effect the serum PSA and alkaline phosphatase levels. However there were no differences between the NQO1 genotypes in the study groups.