The fifth in a series of European workshops for veterinary and human pathologists, “Pathology of the Laboratory Mouse: An International Workshop on Challenges for High Throughput Phenotyping,” was held in Bordeaux, France, from September 30 to October 1, 2010. In this report we outline the rationale for setting up this workshop series, summarize our experience, and suggest approaches for optimizing histopathology phenotyping for gene function discovery.