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Objectives DNA methyltransferase-3B (DNMT3B) plays an important role in the generation of aberrant methylation in carcinogenesis.Polymorphisms of the DNMT3B gene may influence DNMT3B enzyme activity on DNA methylation, thereby modulating the susceptibility to colorectal cancer (CRC).Methods The polymorphisms in the promoter region of the DNMT3B gene [-149C>T (rs2424913) and-579G>T (rs1569686)] were detected by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and a total of 544 CRC patients and 533 age-sex-matched healthy controls were enrolled in the case-control study.Results The results showed that the-579 G allele was associated with a significantly decreased risk of CRC (adjusted OR, 0.50, 95%CI, 0.35-0.72;P=0.0002) when compared with the-579 TT genotype.However, the DNMT3B-149CT genotype was not associated with the risk of CRC (adjusted OR, 0.48, 95%CI, 0.18-1.30;P=0.151).In addition, stratification analysis revealed that the increased risk was predominant in both colon cancer and rectal cancer showing no effect of primary occurrence site.Conclusions Our research demonstrated the-579 G allele was a potential protective factor for the occurrence of CRC.