Objective To study the effect of HBeAg on recurrence and survival after radical resection of small (≤3 cm) hepatocellular carcinoma (HCC). Methods Two hundreds and twenty-three HCC patients undergone radical resection from 1999 to 2000 were divided into two groups according to serum HBeAg status， HBeAg positive group (n=73) and HBeAg negative group (n=150). The patients’ factors, operative factors and tumorous facors were studied retrospectively between the two groups. And risk factors of overall survival (OS) and disease-free survival (DFS) were analyzed. Results There were no significant differences in operative and tumorous factors between the two groups, but the HBeAg positive group were younger with more severe cirrhosis (P=0.004, P=0.008). The OS and DFS were significantly different between the HBeAg positive group and HBeAg negative group. The 1-, 3- and 5-year OS were 91.5%, 76.8%, 60.1% and 95.2%, 85.3%, 73.2%, respectively (P=0.053)； and the 1-, 3- and 5-year DFS were 73.3%, 53.7%, 40.3% and 86.6%, 65.5%, 54.5%, respectively (P=0.002). Multivariate analysis revealed that age ＞50 years, HBeAg positive and macronodular cirrhosis were significantly related to OS, and HBeAg positive, multiple tumor nodulars were significantly related to DFS. Positive serum HBeAg status was an independent risk factor for both OS and DFS. Conclusion Positive serum HBeAg is closely related to early recurrence and survival after radical resection of patients with small HCC.