Objective To investigate the clinical predictors and prognosis of the patients with advanced stage small hepatocellular carcinoma (SHCC) after hepatectomy. Methods A total of 110 patients with SHCC admitted to the General Hospital of PLA and undergone hepatectomy from Jan. 1995 to Dec. 2009 were included in present retrospective study. Survival analysis was performed by Log-rank test and Kaplan-Meier. The association of SHCC and nine routine clinical parameters was analyzed by the univariate and multivariate logistic regression analysis. Results Of the 110 patients with SHCC, 31 (28.2%) were SHCC in advanced stage, and the 1, 3, 5 year survival rates were 78.6%, 61.6% and 38.5%, respectively, with a median survival time of 48.8 months (95% CI 29.2-68.4 months). Seventy-nine of the 110 patients (71.8%) were suffering form early stage SHCC, and the 1, 3, 5 year survival rates were 98.7%, 83.8% and 74.8%, respectively, with a median survival time of 98.0 months (95%CI 73.8-122.2 months). The survival rate was obviously higher in the patients with early stage SHCC than in those with advanced stage SHCC (χ2=13.29, P=0.0003). Multivariate analysis showed that positive AFP was a potential significant predictor of SHCC in advanced stage (RR=14.45; 95%CI 4.05-51.64, P<0.001). Conclusion The SHCC in advanced stage signifies an ominous prognosis. Positive AFP is a potential significant predictor for advanced stage SHCC.