The aetiology of biliary atresia, the leading cause of neonatal extrahepatic jaundice and the main indication for liver transplantation in children, is unknown. Recent research has focused on an infectious aetiology and the development of viral models in animals. The few published epidemiological studies report conflicting results for seasonal, geographical, and racial variations in incidence. In this study, New York State (NYS) Congenital Malformations Registry data from 1983 to 1998 were compared with resident live birth certificate data. County of residence, birth date, gestational age, birthweight, gender, maternal race and maternal age were extracted from the birth certificate data. Isolated and sequence cases were combined for analysis. Observed and expected numbers of cases were calculated by NYS region. Overall, 369 biliary atresia cases were reported in the 16-year study period, a rate of 0.85 [95% CI 0.76, 0.93] per 10,000 live births. Of these, 249 isolated/sequence cases were ascertained, a rate of 0.57 [95% CI 0.50, 0.64] per 10,000 live births. The rate ratio of biliary atresia in New York City (NYC) compared with other NYS was 2.19 [95% CI 1.69, 2.84]. Seasonal patterns varied by region with spring births at highest risk in NYC and September to November births at highest risk in other NYS. The rate ratio in black vs. white mothers was 1.94 [95% CI 1.48, 2.54]. Birthweight and gestational age were associated with biliary atresia with preterm low-birthweight infants at highest risk [RR 3.24, 95% CI 2.20, 4.76]. The association of isolated/sequence biliary atresia with season, preterm birth, and low birthweight in our study supports an infectious disease hypothesis.