CHEK2 mutations have been reported to be associated with different human cancers. However, the genetic defects distribution and the roles of CHEK2 mutations in gastric cancer carcinogenesis remain poorly understood. In this study, we detected two CHEK2 alleles: a protein truncating (1100delC, IVS2+1G>A) and a missense variant (I157T) in 63 unselected gastric cancer cases and 96 healthy controls. The results in this study demonstrated that four SNPs (rs201688553, rs376099090, rs777046932 and rs372452522) in CHEK2 1100delC achieved significant difference in their distributions between gastric cancer cases and controls. Moreover, one polymorphism (rs7289973) and a novel genetic variant (IVS2-372T>C) in CHEK2 IVS2+1G>A regions were identified and demonstrated significant difference in their distributions between gastric cancer cases and controls. Multiple logistic regression analyses revealed that gastric cancer risk were significantly associated with the variant genotypes of the four CHEK2 polymorphisms comparing with their wild-type genotypes. Moreover, it was found that variant rs372452522 in CHEK2 might contribute to susceptibility to lymph node metastasis. Our data demonstrated significant associations between CHEK2 SNPs (rs201688553, rs376099090, rs777046932, rs372452522 and rs7289973) and mutation IVS2-372T>C with gastric cancer. In advance, variant CHEK2 rs372452522 might contribute to lymph node metastasis susceptibility, implying the SNPs and mutation of CHEK2 as potential predictors of cancer susceptibility.