Cytochrome 2E1, has been reported to participate in the pathogenic process of gastrointestinal (GI) cancers. Previous studies showed that the results are conflicting. To clarify the association between cytochrome CY-P2E1 RsaI polymorphism and risk of gastrointestinal cancers, we conducted this meta-analysis of 35 studies with 8267 cases and 11001 controls. Odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the strength of the association. We found that CYP2E1 RsaI polymorphism significantly decreased the risk of GI cancers in heterozygous model (OR = 0.80, 95% CI: 0.66-0.97, P-heterogenecity = 0.027) and dominant model (OR = 0.77, 95% CI: 0.64-0.94, P-heterogenecity = 0.01). In subgroup analysis, CYP2E1 Rsa I polymorphism reduced the risk of esophageal cancer (EC) (allele model: OR = 0.64, 95% CI: 0.49-0.83, P-heterogenecity = 0.001; homozygous model: OR = 0.55, 95% CI: 0.42-0.72, P-heterogenecity < 0.01; heterozygous model: OR = 0.54, 95% CI: 0.36-0.81, P-heterogenecity = 0.003; dominant model: OR = 0.49, 95% CI: 0.33-0.72, P-heterogenecity < 0.01) and cases with GI cancers among the Asians (allele model: OR = 0.79, 95% CI: 0.68-0.91, P-heterogenecity = 0.001; heterozygous model: OR = 0.71, 95% CI: 0.60-0.86, P-heterogenecity < 0.01; dominant model: OR = 0.68, 95% CI: 0.56-0.83, P-heterogenecity < 0.01), but increased the risk of GI cancers in Caucasians (recessive model: OR = 1.53, 95% CI: 1.00-2.34, P-heterogenecity = 0.05). We also confirmed the result in the high-quality studies (heterozygous model: OR = 0.80, 95% CI: 0.65-0.98, P-heterogenecity < 0.01; dominant model: OR = 0.78, 95% CI: 0.64-0.95, P-heterogenecity < 0.01) and in the literatures written in Chinese (allele model: OR = 0.73, 95% CI: 0.54-0.98, P-heterogenecity < 0.01; heterozygous model: OR = 0.66, 95% CI: 0.48-0.92, P-heterogenecity < 0.01; dominant model: OR = 0.66, 95% CI: 0.47-0.94, P-heterogenecity < 0.01). No significant association was observed in the gastric cancer (GC) and colorectal cancer (CRC). Similar results were observed in the subgroup analysis by source of control and pHWE. In conclusion, we suggest that CYP2E1 RsaI polymorphism significantly decreased the risk of GI cancers especially in EC cancer type and in Asians population, but increased risk of GI cancers in the Caucasians.