Abstract.Recently, several studies regarding the association between the pri-miR-124-1 rs531564 polymorphism and cancer susceptibility were explored. Owing to inconsistent results of these studies, a meta-analysis was conducted to determine the association of this polymorphism with cancer risk. Relevant studies were identified by a systematic search of PubMed, EMBASE, Web of Science and CNKI on-line databases. Odds ratios (ORs) and 95% confidence intervals (CIs) from eligible studies were pooled, and heterogeneity and publication bias were also evaluated. A total of five studies with 2,253 cases and 2,510 controls were included in the meta-analysis. Overall, the results showed that the pri-miR-124-1 rs531564 polymorphism was significantly associated with a reduced cancer risk (G vs. C: OR, 0.86; 95% CI, 0.77-0.96; GG vs. CC: OR, 0.52; 95% CI, 0.34-0.79; GG vs. CG/CC: OR, 0.54; 95% CI, 0.36-0.81). Furthermore, in the subgroup analysis by cancer sites, a statistical association was identified between the rs531564 polymorphism and a decreased esophageal squamous cell carcinoma (ESCC) risk (G vs. C: OR, 0.87; 95% CI, 0.77-0.98; GG vs. CC: OR, 0.54; 95% CI, 0.34-0.84). These findings suggested that the genetic variant of rs531564 may have a potential value in decreasing cancer risk, particularly in ESCC patients.