Hepatocellular carcinoma (HCC) is the third most frequent cause of cancer death in South Korea, but genetic susceptibility factors of HCC have not been examined extensively. Methylenetetrahydrofolate reductase (MTHFR) and methionine synthase reductase (MTRR) play an essential role in both DNA synthesis and methylation and polymorphisms in the MTHFR gene, 677C>T, 1298A>C and the MTRR gene, 66A>G, are associated with several types of malignancy. In this study, the allelic frequencies and genotype distribution of three polymorphisms in the MTHFR and MTRR genes from 96 hepatocellular carcinoma (HCC) patients and 201 controls were examined to assess the association between these polymorphisms and the development of HCC in this Korean population. The 66AG+GG (G allele-bearing) genotype of the MTRR gene was significantly associated with an increased risk of HCC (odds ratio, OR, 1.687; 95% confidence interval, CI=1.022-2.787). Moreover, the combination of MTHFR 1298AA/MTRR 66AG+GG (OR=1.854, 95% CI=1.005-3.420) and MTHFR 1298AC+CC/MTRR 66AG+GG (OR=2.733, 95% CI=1.195-6.249) showed a significant association with HCC risk. In the data classified by age and etiology, MTRR 66A>G over the age of 65 years, MTHFR 1298A>C under the age of 65 years and the MTRR 66AG+GG genotype in the hepatitis B virus (HBV) patients were increased risk factors for the disease. The MTHFR 1298A>C and the MTRR 66A>G genotypes were associated with an increased risk of HCC in this Korean population. Further studies involving larger and varied populations could provide a potential tool for cancer risk assessment in patients who are at risk of developing HCC.