Eduard Pernkopf's Topographical Anatomy of Man has been a widely used standard work of anatomy for over sixty years. International inquiries about the National Socialist (NS) political background of Eduard Pernkopf and the use of bodies of NS victims for the atlas were first directed at the University of Vienna in 1996. A public discussion about the further use of the book followed and led to the creation of the Senatorial Project of the University of Vienna in 1997. This historical research project confirmed the strong NS affiliation of Pernkopf and revealed the delivery of at least 1,377 bodies of executed persons to the Anatomical Institute of Vienna during the NS time. The possible use of these bodies as models cannot be excluded for up to half of the approximately 800 plates in the atlas. In addition tissue specimens from NS victims were found and removed from the collections of the Viennese Medical School and received a burial in a grave of honor. The Pernkopf controversy facilitated the historical and ethical analysis of the anatomical sciences in Austria and Germany during the NS regime. The continued use of the Pernkopf atlas is not only justifiable but desirable as a tool in the teaching of anatomy, history, and ethics.