Inbred strains are the raw material for the generation of Genetically Engineered Mice (GEM) that have become indispensable tools for cancer research, and for the identification of genes involved in human diseases. The "German Mouse Clinic" was designed to provide the scientific community with a systematic, standardized and comprehensive phenotyping of mouse models on various genetic backgrounds and generated by different methods (transgenic, knockouts, ENU mutagenesis screen and gene-trap approaches). The pathology screen within the German Mouse-Clinic was conceived to ensure a complete morphologic phenotype of mouse models, to support discovery of genes functions, and to understand how these genes influence the development of human diseases. The goal is to define disease entities that can be recognized by a pathologist and relate them to human disorders when possible. Knowing the inherent morphologic phenotype of the most frequent used mouse strains is of utmost importance for the correct interpretation of mouse models. The main challenges, which pathologist are confronted to validate mouse models for human diseases include (1) knowledge of mouse biology and of histological differences between mouse strains and humans, (2) the terminology that should be used for the classification of neoplastic lesions in GEM's, (3) to asses the usefulness of a particular GEM as model for a human disease.