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BACKGROUND We have recently reported that simultaneous determination of the fucosylation and glucosaminylation of alpha-fetoprotein (AFP) was useful in the differential diagnosis of various liver diseases. Here, we measured these indices in germ cell tumor and compared them with those in various diseases to reveal the characteristic feature of the carbohydrate moiety of AFP in this tumor. METHODS Fucosylation and glucosaminylation indices of AFP were determined for 743 serum samples from 10 patients with germ cell tumor, 437 with hepatocellular carcinoma (HCC), 241 with benign liver diseases (24 patients with acute viral hepatitis, 99 with chronic hepatitis, and 118 with hepatic cirrhosis), and 55 with carcinoma metastatic to the liver from digestive organs (41 from stomach, 10 from gallbladder, 2 from pancreas, and 2 from colon) by crossed immunoaffinoelectrophesis in the presence of concanavalin A and Lens culinaris agglutinin. RESULTS The fucosylation index of AFP in germ cell tumors (99% +/- 2%, mean +/- SD) was higher than those in HCC (39% +/- 31%), carcinoma metastatic to the liver (76% +/- 27%), and benign liver diseases (4% +/- 7%); the differences were statistically significant (P < 0.001). The glucosaminylation index of AFP in germ cell tumor (45% +/- 20%) also was significantly higher than those in HCC (4% +/- 4%) and in benign liver diseases (1% +/- 4%) (P < 0.001). The difference in mean percentage of the glucosaminylation index, however, was not significant between germ cell tumors (45% +/- 20%) and carcinoma metastatic to the liver (39% +/- 23%). CONCLUSIONS The current study indicates that the most characteristic feature of glycosylation of AFP in germ cell tumors is fucosylation rather than glucosaminylation.