The formation of a skeleton with its numerous bones of various shapes and sizes and the growth of these bones from embryonic to adult size is a complex process involving a multitude of genes. The complexity of the process is reflected by the large number of inherited diseases with skeletal phenotypes (in man and mouse) as well as by the ever-increasing number of genes shown to be involved in skeletal morphogenesis (for review, see refs. 1,2). The inactivation of genes through transgenic mouse technology has become a popular method of analyzing the function of newly discovered genes. Such mice may have expected or unexpected phenotypes and, considering the large number of genes involved, skeletal alterations are commonly found. Naturally, the question arises, What is the role of this gene in skeletal morphogenesis and how can the pheno-type be explained. This chapter will address these questions and will supply the investigator with a conceptual framework for how to investigate skeletal defects in the mouse.