Hepatocellular carcinoma only rarely occurs in Alagille syndrome. Here, we report on three cases of hepatocellular carcinoma associated with Alagille syndrome. All three patients were boys and presented with jaundice. In addition, they had the characteristic facial appearance of Alagille syndrome with cardiac, vertebral, and eye anomalies, and all had passed acholic stools from the neonatal period. Liver biopsies were diagnosed as bile duct paucity, compatible with Alagille syndrome in two cases, but the third case showed marked bile duct proliferation at the initial liver biopsy when 7 months old, which made diagnosis difficult. Eventually, all three cases progressed to biliary cirrhosis and hepatocellular carcinoma, which occurred at 17 months, 4 years, and 7 years, respectively. Because of the unusual liver histology and early onset of hepatocellular carcinoma, careful clinicopathologic correlations and close monitoring are required for the diagnosis of Alagille syndrome and for the early detection of hepatocellular carcinoma.