He graduated with an MD, PhD, from the Technical University of Munich, where he trained in developmental genetics in the laboratory of Rudi Balling. After completing his residency in neuropathology and general pathology at the University of Bonn, he became a postdoctoral fellow in the laboratory of Rudolf Jaenisch at the Whitehead Institute for Biomedical Research. Wernig received an NIH Pathway to Independence Award, the Cozzarelli Prize for Outstanding Scientific Excellence from the National Academy of Sciences USA, the Outstanding Investigator Award from the International Society for Stem Cell Research, the New York Stem Cell Foundation Robertson Stem Cell Prize, and more recently has been named an HHMI Faculty Scholar.