OBJECTIVE The aim of this study was to investigate the incidence, clinical course, and outcome of multiple intrahepatic biliary cysts in patients with biliary atresia. METHODS From 1992 to 2000, 154 patients with biliary atresia were examined for intrahepatic cysts. They were followed and examined routinely using abdominal ultrasonography. RESULTS Twenty-three patients had single intrahepatic cysts, and 16 patients had multiple cysts. The incidence of intrahepatic cysts in these patients were 25.3% (39 of 154) for all kinds of cysts and 10.4% (16 of 154) for multiple intrahepatic cysts. Of the 16 patients with multiple cysts, 13 (81.3%) had jaundice, and 15 (93.8%) had a history of cholangitis before cysts were detected. Image studies showed multiple discrete ovoid or round intrahepatic biliary cysts with various sizes along the biliary trees. The cysts decreased in size or number in 7 patients after antibiotic treatment and disappeared in only one patient. The mortality rate was higher in patients with multiple cysts than in those with single cysts (P =.037). CONCLUSIONS Multiple intrahepatic biliary cysts are a common complication in patients with biliary atresia and suggests a poor prognosis. Prolonged parenteral antibiotics treatment should be administered when signs of biliary infection appear.