Folate deficiency has been associated with certain types of human cancer. We therefore investigated the effects of genetic polymorphisms in folate-metabolizing enzymes on the risk of developing gastroesophageal cancers in a Chinese population where folate deficiency is common. We found that functional polymorphisms in methylenetetrahydrofolate reductase (MTHFR) and thymidylate synthase (TS), two key enzymes involved in folate and methyl group metabolism, were significantly associated with increased risk of esophageal squamous cell carcinoma, gastric cardia carcinoma, and pancreatic carcinoma. The polymorphisms modulate risk of these cancers associated with low folate status. Our results suggest that MTHFR and TS genotypes may be determinant of gastroesophageal cancers in this at-risk Chinese population.