Previous studies have focused on the association of a gene (EPHX1) encoding microsomal epoxide hydrolase with the carcinogenesis of hepatocellular carcinoma (HCC). In the present study, we performed a meta-analysis to systematically summarize the possible association between EPHX1 genetic polymorphisms and the risk for HCC. We conducted a search of case-control studies on the associations of EPHX1 genetic polymorphisms with susceptibility to HCC in PubMed, EMBASE, ISI Web of Science, Wanfang database in China, and the Chinese National Knowledge Infrastructure databases. Data from eligible studies were extracted for meta-analysis. HCC risk associated with EPHX1 genetic polymorphism was estimated by pooled odds ratios and 95% confidence intervals. Thirteen studies were included in the present meta-analysis. Our results showed that, for the two polymorphisms (337 T > C and 416A > G) of EPHX1 gene, neither allele frequency nor genotype distributions were associated with risk for HCC in all genetic models (all P > 0.05). This meta-analysis suggests that EPHX1 genetic polymorphisms were not associated with the risk of HCC.