Our previous immunohistochemical studies in the pancreas, intrahepatic bile duct, and ampulla of Vater demonstrated that an invasive carcinoma with a poor outcome showed a pattern of MUC1 (membrane-bound mucin) positive and MUC2 (intestinal-type secretory mucin) negative, whereas many of the non-invasive tumors with favorable outcome showed a pattern of MUC1 negative and MUC2 positive. The aim of this study is to compare the expression profiles of MUC1 and MUC2 mucins in extrahepatic bile duct carcinomas to gain insight into the relationship between the biological nature of the carcinomas and the role of mucins. We examined the expression profiles of MUC1 of different glycoforms and MUC2 in 60 extrahepatic bile duct carcinomas using immunohistochemistry.The expression of MUC1/CORE (core peptide of MUC1), MUC1/DF3 (core peptide of MUC1 with sialyl oligosaccharides) and MUC1/MY.1 E12 (sialylated MUC1) showed a significant relationship with tumor progression factors such as poor differentiation, deep invasion, lymph node metastasis, lymphatic invasion or perineural invasion. In contrast, the expression of MUC1/HMFG-1 (fully glycosylated MUC1) did not show a significant relationship with the tumor progression factors. In the different glycoforms of MUC1 examined, the expression of MUC1/DF3 and MUC1/MY.1E12 was related with the poor outcome of the patients. In contrast, the expression of MUC2 was inversely related with the tumor progression factors and poor outcome. In the 52 patients with advanced tumors, only MUC1/DF3 high expression correlated with poor prognosis. In conclusion, MUC1/DF3 was the most useful prognosis indicator among the various glycoforms of MUC1 mucins.