MicroRNAs (miRNAs) bind to the 3-untranslated regions (3-UTRs) of mRNAs, affecting translation and regulating cell differentiation, tumorigenesis and apoptosis. Genetic polymorphisms in these regions in target genes are able to affect the binding affinity between miRNA and target genes, ultimately affecting the expression of individual miRNAs. In the present case-control study, genotyping of 5 microRNA single nucleotide polymorphisms (SNPs) located at the binding site of the 3-UTR of RYR3 (rs1044129), C14orf101 (rs4901706), KIAA0423 (rs1053667), GOLGA7 (rs11337) and KRT81 (rs3660) genes was assessed in order to investigate its role in gastric cancer (GC). The results indicated that the rs4901706 SNP, which is located in the 3-UTR of C14orf101, was associated with GC development risk, as determined by (2) analysis (relative risk, 1.630; 95% confidence interval, 1.070-2.483; P=0.022). A Renilla/luciferase reporter assay also indicated the different binding affinity between the SNP of rs4901706 and microRNA. In conclusion, rs4901706 SNP of C14orf101 gene in the microRNA binding site may be used as a valuable biomarker when predicting GC risk.