In Taiwan, a screening system using an infant stool color card to promote the early diagnosis of biliary atresia (BA) was established in 2002. This study aimed to investigate the 5-year outcome of BA before and after using the screening program. BA patients were divided into three cohorts according to their birth dates. The patients in cohort A (n = 89) were born before the stool card screening program (1990-2000); those in cohort B (n = 28) were screened by the stool card regional screening program (2002-2003); and those in cohort C (n = 74) were screened by the stool card universal screening program (2004-2005). The relative odds ratios were computed using logistic regression to compare the different factors affecting survival time. The rate of age at Kasai operation <60 days was 49.4% and 65.7% in cohorts A and B+C, respectively (P = 0.02). The jaundice-free (total serum bilirubin <2.0 mg/dL) rate 3 months after surgery was 34.8% and 60.8% in cohorts A and B+C, respectively (P < 0.001). The 3-year jaundice-free survival rate with native liver was 31.5% in cohort A and 56.9% in cohort B+C (P < 0.001), whereas the 3-year overall survival rates were 64.0% and 89.2%, respectively (P < 0.001). The 5-year jaundice-free survival rate with native liver was 27.3% in cohort A and 64.3% in cohort B (P < 0.001), and the 5-year overall survival rates were 55.7% and 89.3%, respectively (P < 0.001). CONCLUSION: The stool color card screening program for BA allows for earlier Kasai operation, which increases the jaundice-free rate at 3 months postsurgery. With higher surgical success rates, the 3- and 5-year outcome of BA patients in Taiwan improves remarkably.