The Collaborative Cross(CC) is a powerful genetic resource with a wide range of applications in medical research. It is a multiparental genetic reference population, composed of 200 recombinant inbred mouse strains. It was designed to be a resource for rapid mapping of genes that mediate complex traits. The CC has been produced following an intense breeding program that had taken over ten years to complete. It is now becoming available to the research community. While advances in human genetic technologies over the last decade have been substantial, the CC provides the ability to make discoveries not possible with other methods or resources. It can be applied to any subject that can be measured or modelled in the mouse. Here, we discuss a range of applications for which the CC can be used, with examples taken from the early characterization of this powerful resource.