Objective: To study the clinical and prognostic features of non-B non-C alpha-fetoprotein (AFP) (-)-hepatocellular carcinoma (HCC) (NBNC-AFP(-)-HCC), and the relationship between the prognostic features of HCC and hepatitis B virus surface antigen (HBsAg) status and AFP. Methods: We enrolled 227 patients underwent hepatic resection for HCC between January 1998 and December 2007 in Sun Yat-Sen University Cancer Center, all of them were diagnosed with HCC by pathology. All patients were stratified into one of four groups (B-AFP(+)-HCC, B-AFP(-)-HCC, NBNC-AFP(+)-HCC, and NBNC-AFP(-)-HCC) according to AFP levels and HBsAg status. The clinicopathologic and survival characteristics of NBNC-AFP(-)-HCC patients were compared with all other three groups. Results: Out of the 105 NBNC-HCC patients, 43 patients (40.9%) were AFP-negative HCC. There were some differences in factors between the B-AFP(+) and NBNC-AFP(-) patients, such as age, body mass index (BMI), diabetes, and ALT (P<0.05). On univariate analysis, tumor size, secondary tumor, and portal invasion were prognostic factors for overall survival (OS) and disease-free survival (DFS) (P<0.05). Cox multivariate regression analysis suggested that tumor size and tumor number (P<0.05) were independent predictors. In addition, compared with that in the B-AFP(+)-HCC, B-AFP(-)-HCC, and NBNC-AFP(+)-HCC groups, the NBNC-AFP(-)-HCC patients had the best DFS (P<0.05). Compared with that in the B-AFP(+)-HCC and NBNC-AFP(+)-HCC groups, the NBNC-AFP(-)-HCC patients had better OS(P<0.05), and survival rates were similar to those of B-AFP(-)-HCC patients. Conclusion: NBNC-AFP(-)-HCC patients had a relatively favorable prognosis. It can serve as a useful marker in predicting the risk of tumor recurrence in the early stages.