The objective of this study was to describe the congenital anomalies in 17 Canadian neonatal intensive care units (NICUs) and their impact on mortality, morbidity, and resource utilization. This study was performed using a database analysis of 19,507 consecutive admissions. Results show that 13.7% of admissions had one or more anomalies. There was wide variation in incidence between NICUs (4.4 to 36.6%). Congenital anomalies were associated with increased severity of illness, and higher mortality, morbidity, and resource use. Inclusion of congenital anomalies improves mortality prediction in regression analyses models. Congenital anomalies have a significant impact on NICU outcomes and resource use.