The number and ratio of both HBsAg- and HCV Ab-negative hepatocellular carcinoma (HCC-nonBC) cases have been steadily increasing in Japan. The aim of this study was to examine the frequency of detection of HCC-nonBC by screening methods and to elucidate the clinical characteristics of HCC-nonBC compared with those of hepatitis C and/or B virus-associated HCC (HCC-virus). We recruited 624 patients with HCC who were diagnosed between 1982 and 2007 at the Department of Gastroenterology and Hepatology, Nagasaki University Hospital. They were categorized into 2 groups as follows: i) 550 were included in the HCC-virus group: positive for HBsAg and/or positive for HCV Ab, and ii) 74 were included in the HCC-nonBC group: negative for both HBsAg and HCV Ab. The follow-up patterns until the initial detection of HCC and the survival rates were analyzed and compared between the 2 groups. Multivariate analysis identified follow-up, alcohol consumption, albumin level, total bilirubin level, alpha-fetoprotein (AFP) level, and tumor-node-metastasis (TNM) stage as independent and significant risk factors for prognosis. Among the 397 patients with HCC in TNM stage I or II, multivariate analysis identified the cause of liver disease, gender, Child-Pugh score, serum albumin level and TNM stage as independent and significant risk factors for prognosis. We reported that the poor prognoses of patients with HCC-nonBC were attributable to its late detection in an advanced condition due to the absence of a surveillance system for the early detection of HCC. However, in early-stage patients, patients with HCC-nonBC showed significantly better prognosis than those in the HCC-virus group.