Objectives To prospectively assess the value of serum total bilirubin (TB) within 3 months of hepatoportoenterostomy (HPE) in infants with biliary atresia as a biomarker predictive of clinical sequelae of liver disease in the first 2 years of life. Study design Infants with biliary atresia undergoing HPE between June 2004 and January 2011 were enrolled in a prospective, multicenter study. Complications were monitored until 2 years of age or the earliest of liver transplantation (LT), death, or study withdrawal. TB below 2 mg/dL (34.2 μM) at any time in the first 3 months (TB <2.0, all others TB ≥2) after HPE was examined as a biomarker, using Kaplan-Meier survival and logistic regression. Results Fifty percent (68/137) of infants had TB <2.0 in the first 3 months after HPE. Transplant-free survival at 2 years was significantly higher in the TB <2.0 group vs TB ≥2 (86% vs 20%, P <.0001). Infants with TB ≥2 had diminished weight gain (P <.0001), greater probability of developing ascites (OR 6.4, 95% CI 2.9-14.1, P <.0001), hypoalbuminemia (OR 7.6, 95% CI 3.2-17.7, P <.0001), coagulopathy (OR 10.8, 95% CI 3.1-38.2, P =.0002), LT (OR 12.4, 95% CI 5.3-28.7, P <.0001), or LT or death (OR 16.8, 95% CI 7.2-39.2, P <.0001). Conclusions Infants whose TB does not fall below 2.0 mg/dL within 3 months of HPE were at high risk for early disease progression, suggesting they should be considered for LT in a timely fashion. Interventions increasing the likelihood of achieving TB <2.0 mg/dL within 3 months of HPE may enhance early outcomes. Trial registration ClinicalTrials.gov: NCT00061828 and NCT00294684.