Epidemiologic findings concerning the association between the hsa-mir-499 rs3746444 A>G polymorphismand cancer risk have yielded mixed results. We aimed to investigate the association by performing a meta-analysisof all available studies. We searched PubMed and EMBASE for studies published up to November 2014, usingodds ratios (ORs) with 95% confidence intervals (CIs) to assess the strength of any association. The Benjamini-Hochberg (BH) method was used to correct the p values for multiple comparisons. We included 39 studies,including 14,136 cases and 16,937 controls. The results of overall meta-analysis suggested a borderline associationbetween hsa-mir-499 rs3746444 polymorphism and cancer susceptibility (AG+GG vs. AA: OR=1.15, 95% CI=1.04-1.26, corrected p value=0.04). After removing studies not conforming to Hardy–Weinberg equilibrium(HWE), however, this association disappeared (AG+GG vs AA: OR=1.18, 95% CI=1.03-1.34, corrected pvalue=0.21). When stratified analysis by ethnicity, cancer type or HWE in controls, although some associationsbetween hsa-mir-499 rs3746444 polymorphism and cancer susceptibility were detected, these associations nolonger existed after adjustment using BH method. In conclusion, our meta-analysis suggests that hsa-mir-499rs3746444 A>G polymorphism is not associated with risk of cancer based on current evidence.