Biliary atresia (BA) is a significant liver disease in children. Since 2004, Taiwan has implemented a national screening program that uses an infant stool color card (SCC) for the early detection of BA. The purpose of this study was to examine the outcomes of BA cases before and after the launch of this screening program. The objectives of this study were to evaluate the rates of hospitalization, liver transplantation (LT), and mortality of BA cases before and after the program, and to examine the association between the hospitalization rate and survival outcomes.This was a population-based cohort study. BA cases born during 1997 to 2010 were identified from the Taiwan National Health Insurance Research Database. Sex, birth date, hospitalization date, LT, and death data were collected and analyzed. The hospitalization rate by 2 years of age (Hosp/2yr) was calculated to evaluate its association with the outcomes of LT or death.Among 513 total BA cases, 457 (89%) underwent the Kasai procedure. Of these, the Hosp/2yr was significantly reduced from 6.0 to 6.9/case in the earlier cohort (1997-2004) to 4.9 to 5.3/case in the later cohort (2005-2010). This hospitalization rate reduction was followed by a reduction in mortality from 26.2% to 15.9% after 2006. The Cox proportional hazards model showed a significant increase in the risk for both LT (hazard ratio [HR] = 1.14, 95% confidence interval [CI] = 1.10-1.18) and death (HR = 1.05, 95% CI = 1.01-1.08) for each additional hospitalization. A multivariate logistic regression model found that cases with a Hosp/2yr >6 times had a significantly higher risk for both LT (adjusted odds ratio [aOR] = 4.35, 95% CI = 2.82-6.73) and death (aOR = 1.75, 95% CI = 1.17-2.62).The hospitalization and mortality rates of BA cases in Taiwan were significantly and coincidentally reduced after the launch of the SCC screening program. There was a significant association between the hospitalization rate and final outcomes of LT or death. The SCC screening program can help reduce the hospitalization rate and mortality of BA cases and bring great financial benefit.