Autopsies after neonatal death due to suspected or insufficient diagnosed cardiac malformations provide important information to parents and the involved obstetric and pediatric physicians. The autopsy rate, however, is declining. Postmortem magnetic resonance imaging may be an alternative option for selected cases, providing detailed morphologic information about the cardiovascular system. This case report demonstrates the beneficial use of postmortem magnetic resonance imaging in a newborn with a suspected complex cardiac malformation. The magnetic resonance imaging was able to complete the diagnosis of situs inversus totalis, with transposition of great arteries, and to provide valuable information about the underlying physiology.