This study investigated the genetic causes of early death in a 3-year death cohort from the NICU of Children’s Hospital of Fudan University. We identified 44 (19.7 %, 44/223) deceased newborns with genetic findings and 13 of them had medically actionable disorders based on genetic diagnosis. Multiple congenital malformation was the leading genetic cause of death in NICU. Our findings provide a comprehensive perspective on the genetic causes of neonatal mortality, emphasize the importance of genetic testing in NICU to gain evidence for early accurate diagnosis and precise genetic counseling for the patient’s family. (By Drs. Xu Liu and Lin Yang, https://jmg.bmj.com/content/early/2019/09/20/jmedgenet-2019-106221 )