MicroRNAs (miRNAs) are an abundant class of small non-protein-coding RNAs with posttranscriptional regulatory functions as tumor suppressors and oncogenes. It has been suggested that the presence of single nucleotide polymorphisms (SNPs) in miRNAs can alter miRNA processing, expression, and/or binding to target mRNA and represent another type of genetic variability that can contribute to susceptibility to cancer development in humans. An adenine to guanine polymorphism (rs3746444), located in the sequence of miR-499, results in a change from A:U to G:U in its stem region. To determine the association of this polymorphism with the risk of hepatocellular carcinoma (HCC) in a Turkish population, a hospital-based case-control study was designed consisting of 222 subjects with HCC and 222 cancer-free control subjects matched for age, gender, smoking and alcohol status. The genotype frequency of the miR-499 rs3746444 polymorphism was determined using a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay. No statistically significant differences were found in the allele or genotype distributions of the miR-499 rs3746444 polymorphism among HCC and cancer-free control subjects (P>0.05). Our results demonstrate for the first time that the miR-499 rs3746444 polymorphism does not been any major role in genetic susceptibility to hepatocellular carcinogenesis, at least in the population studied here. Independent studies are need to validate our findings in a larger series, as well as in patients of different ethnic origins.