This study aimed to determine the clinical significance of the NQO1 C609T (rs1800566, Pro187Ser) polymorphism in patients with colorectal cancer (CRC) in the Azerbaijani population. 142 patients with CRC and 146 healthy individuals were included in the study. DNA from blood was isolated using the salting-out method, and genotypes were determined on agarose gel using the PCR-RFLP method. When comparing the patients and control groups, heterozygous CT (OR=1.813; 95%CI=1.097– 2.995, P=0.020), under the dominant model (OR=1.842; 95%CI=1.137–2.983, P=0.013), and the mutant T allele (OR=1.644; 95%CI=1.096–2.465, P=0.016) were statistically associated with an increased risk of CRC. When comparing male patients with healthy men, heterozygous CT was associated with a higher risk of CRC (OR=2.219; 95%CI=1.079-4.565, P=0.029). However, the age, pathological tumor grade and stage, smoking, and alcohol consumption of the study groups were compared and no significant relationship was found (P>0.05). Our findings showed that the NQO1 C609T polymorphism is related to the risk of colorectal cancer in the Azerbaijan population.