To determine if common clinical factors are associated with the neonatal autopsy rate, we conducted a retrospective analysis of 117 deaths in a neonatal intensive care unit. The autopsy rate of neonatal deaths was significantly greater than the autopsy rate of adult and non-neonatal pediatric deaths. In the newborn period, the autopsy rate of transported patients was significantly less than that of inborn patients. Among those transported, autopsies were significantly less common in patients of low birth weight or low gestational age. Furthermore, among all newborns dying within two days of admission, transported patients were less likely to undergo autopsies than inborn patients. Other factors, including maternal age, race, and marital status, did not affect the autopsy rate of newborn deaths. These data suggest that early separation of the mother from her infant and the medical team caring for the infant adversely affect the process of autopsy request and consent.