Objective To investigate the prognosis of patients with primary liver cancer in different pathological types after hepatectomy, and to analyze the effects of clinicopathological factors on the survival. Methods The clinical data of 567 patients with primary liver cancer who received hepatectomy at the Affiliated Hospital of Qingdao University from January 1997 to December 2008 were retrospectively analyzed. All patients were divided into hepatocellular carcinoma (HCC) group, cholangiocarcinoma (CC) group and combined hepatocellular carcinoma and cholangiocarcinoma (cHCC CC) group. The survival and risk factors of the patients were analyzed. All data were analyzed by using the chi square test, t test, analysis of variance. The survival curve was drawn by the Kaplan Meier method and the survival of the 3 groups was compared by the Log rank test. The risk factors were analyzed by the one way analysis of variance and COX regression model. Results The Results of pathological examination confirmed that 92.9%(527/567) patients were with HCC, 4.6%(26/576) with CC and 2.5%(14/567) with cHCC CC. The median cumulative survival time of patients with HCC was 48 months, which was significantly longer than 19 months of patients with CC and 14 months of patients with cHCC CC (Log rank value=4.354, 8.847, P <0.05). The median tumor free survival time of patients with HCC was 26 months, which was significantly longer than 9 months of patients with CC and 9 months of patients with cHCC CC (Log rank value=6.479, 7.708, P <0.05). The tumor recurrence rate within 1 year of patients with HCC was 28.8%(152/527), which was significantly lower than 57.7%(15/26) of patients with CC or 9/14 of patients with cHCC CC ( F= 17.046, P <0.05). No vascular thrombosis was detected in patients with CC, but the regional lymph node metastasis rate was 19.2%(5/26), which was significantly higher than 2.8%(15/527) of patients with HCC (χ 2= 19.082, P <0.05). Level of alpha fetoprotein, TNM staging, tumor diameter, multiple foci, liver capsule invasion, satellite foci and lymph node metastasis were risk factors for the survivals of patients with primary liver cancer after hepatectomy (χ 2=8.648, 118.786, 59.548, 7.639, 13.200, 43.842, 15.540, P <0.05). Vascular tumor thrombosis and Child Pugh classification were the risk factors for the survivals of patients with HCC or cHCC CC (χ 2=70.446, 6.230, P <0.05). TNM staging, tumor diameter, satellite foci and vascular tumor thrombusis were the independent risk factors for the survivals of patients with primary liver cancer ( RR=1.420, 1.050, 1.513, 1.899, P <0.05); TNM staging, tumor diameter and vascular tumor thrombosis were the independent risk factors for the survivals of patients with HCC ( RR=1.432, 1.888, 1.052, P <0.05). TNM staging and tumor diameter were the independent risk factors for the survivals patients with CC( RR=1.473, 1.503, P <0.05). Conclusion Although CC and cHCC CC take small proportion in the primary liver cancer, the tumor recurrence rate is higher and the survival rate is lower when compared with patients with HCC.