The microarrays were fabricated to explore the relationship between methylenetetrahydrofolate reductase (MTHFR) polymorphisms (C677T and A1298C) and risk of gastric carcinoma in Chinese population. The genomic DNA was isolated from 170 patients with gastric carcinoma and 140 age- and sex-matched control subjects. The frequencies of C677T genotype were: CC (47.9%), CT (40%), CT (12.1%) in control group and CC (35.9%), CT (45.9%), TT (18.2%) in gastric carcinoma group, respectively. The individuals with 677CT + TT or 677TT genotypes had a 1.67-fold (95% CI: 1.06-2.64) or 2.67-fold (95% CI: 1.382-5.341) increased risk of developing gastric carcinoma compared with those carrying 677CC genotype. The genotype of MTHFR gene A1298C allele was not significantly different between the two groups. We found that a joint effect exits between the MTHFR C677T and A1298C polymorphism on the risk of gastric carcinoma. Our results show that the single nucleotide polymorphisms in the MTHFR gene are associated with the risk of gastric carcinoma in the east China population.