Radical resection for patients with peripheral cholangiocarcinoma is rare. Prognostic factors related to survival with peripheral cholangiocarcinoma after hepatectomy have not yet been reported. Of 41 hepatectomized patients with peripheral cholangiocarcinoma, a computer analysis of 14 clinicopathological factors on patients survival was performed with univariate and multivariate analysis. Median and mean survival times for patients with peripheral cholangiocarcinoma after hepatectomy were 12.0 and 22.8 months. The 1-, 2-, 3-, 4- and 5-year survival rates were 53.7%, 39.0%, 36.6%, 26.8%, and 26.8% respectively. Univariate analysis of overall survival involving all patients identified 7 factors that were associated with a significantly outcome: mucobilia (p = 0.043), capsular invasion (p = 0.007), tumor spreading type (p = 0.0003), section margin (p = 0.001), histologic type (p = 0.008), macroscopic and microscopic vascular involvement (p = 0.031), and lymphatic invasion (p = 0.004). With multivariate analysis using the COX stepwise proportional hazards model, only mucobilia, tumor spreading type and section margin were significantly related to prognosis. Intrahepatic bile duct carcinoma patients with mucobilia, intraductal papillomatosis and a tumor-free margin after hepatectomy had a better prognosis.