For her discovery of genes that control the development of animals and humans, as well as for demonstrating morphogenetic gradients in the fruit fly embryo, Christiane Nüsslein-Volhard has received numerous honours, honorary doctorates, and awards, including the Gottfried Wilhelm Leibniz Prize of the German Research Foundation (1986), the Albert Lasker Medical Research Award (1991), and the Nobel Prize in Physiology or Medicine (1995). She is a member of the Royal Society (UK), the National Academy (USA), the Order Pour le Mérite (Germany), the Leopoldina (Germany), the Berlin-Brandenburg Academy (Germany), the Curia of Science (Austria), and the Académie des Sciences (France). From 2001 to 2006, she was a member of the German Ethics Council of the Federal Government.
In 2004, she founded the Christiane Nüsslein-Volhard-Foundation to support young female scientists with children. In 2008, she served as President of the Society of German Natural Scientists and Physicians, and from 2005 to 2009 as Secretary-General of the European Molecular Biology Organisation (EMBO). From 2005 to 2012, she was a member of the Scientific Council of the European Research Council (ERC) of the European Union. From 2013 to 2021, she served as Chancellor of the Ordre Pour le Mérite. In 2016, she was awarded an Advanced Grant by the European Research Council (ERC).
She is Chair of the Board of Trustees of the International Hugo Wolf Academy e.V., Stuttgart.