Association of gene alterations and prognosis has not fully been elucidated in hepatocellular carcinoma (HCC). To clarify the relationship between p53 and hMSH2 mutations and prognosis, we analysed these mutations in 83 HCC cases and assessed their association with various clinicopathological factors. The 3-year disease-free survival (DFS) or overall survival (OS) rates in HCC patients with p53 mutation and p53 wild/hMSH2 mutation significantly decreased compared with those without these mutations (14.3% and 37.5% versus 67.5% for DFS; 35.7% and 50.0% versus 96.4% for OS, respectively). In the multivariate analysis, categories by p53 and hMSH2 mutation status, and liver cirrhosis demonstrated statistical significances for DFS and OS. Moreover, the frequency of patients with p53 and/or hMSH2 mutations in intrahepatic metastasis (75.0%) was significantly higher than that in multicentric occurrence (14.3%). Thus, p53 and hMSH2 mutations will be useful for identifying subsets of HCC patients with poor prognosis.