The objective of this study was to determine the outcomes of Croatian children with biliary atresia. Health records of infants born in Croatia between January 1, 1992 and December 31, 2006 who were diagnosed with biliary atresia and treated at a single university center were reviewed. Survival rates were calculated with the Kaplan-Meier method. Twenty-nine patients with biliary atresia were identified. Incidence was one in 23,600 live births (95% confidence interval 1/17,400-1/27,200). The median age at Kasai operation was 66 days (range 22-192). Median follow-up was 2.65 years (range 0.2-14.3). Overall survival rates for the patients who underwent Kasai portoenterostomy, including those six (20%) who subsequently underwent liver transplantation, were 75.6%. Five and 10-year native liver survival rates were 51.7% and 38.8%, respectively (median survival time was 7.88 years). Survival rate curves in two groups of patients according to the biliary atresia phenotype (fetal or perinatal form) were divergent. Survival was 87.7% in perinatal form and 43.8% in fetal form (Breslow chi-square 8.082, p < 0.01). Overall survival rates of patients with biliary atresia in Croatia compared unfavorably with current international standards; this could be improved with earlier referral for liver transplantation. Results of Kasai operation (native liver survival rates) compared favorably with results reported elsewhere.