Systemic phenotyping of mutant mice has been established at large scale in the last decade as a new tool to uncover the relations between genotype, phenotype and environment. Recent advances in that field led to the generation of a valuable open access data resource that can be used to better understanding the underlying causes for human diseases. From an ethical perspective, systemic phenotyping significantly contributes to the reduction of experimental animals and the refinement of animal experiments by enforcing standardisation efforts. There are particular logistical, experimental and analytical challenges of systemic large-scale mouse phenotyping. On all levels, IT solutions are critical to implement and efficiently support breeding, phenotyping and data analysis processes that lead to the generation of high-quality systemic phenotyping data accessible for the scientific community.