To examine the relative contributions of preterm delivery and congenital anomalies to neonatal mortality.Retrospective analysis of 2009-2011 linked birth cohort-hospital discharge files for California, Missouri, Pennsylvania and South Carolina. Deaths were classified by gestational age and three definitions of congenital anomaly: any ICD-9 code for an anomaly, any anomaly with a significant mortality risk, and anomalies recorded on the death certificate.In total, 59% of the deaths had an ICD-9 code for an anomaly, only 43% had a potentially fatal anomaly, and only 34% had a death certificate anomaly. Preterm infants (37 weeks GA) accounted for 80% of deaths; those preterm infants without a potentially fatal anomaly diagnosis comprised 53% of all neonatal deaths. The share of preterm deaths with a potentially fatal anomaly decreases with GA.Congenital anomalies are responsible for about 40% of neonatal deaths while preterm without anomalies are responsible for over 50%.