The vertebrate gut is a specialized structure responsible for the intake and digestion of food, absorption of nutrients, and expulsion of waste products. The organs of the digestive tract have been conserved over time, but modifications to the size and shape of individual structures exist within the different vertebrate lineages. The skate’s spiral intestine has evolved to maximize nutrient absorption within a compact structure to create space in the body cavity for the organs needed for buoyancy. Studying the unique intestinal morphology of Leucoraja erinacea, or the little skate, provides an opportunity to understand the role of differential gene expression in development. The vertebrate digestive system develops from the embryonic gut tube through the expression of specific genes that direct the development of different tissue types and organs at specified locations. The genes Shh, Wnt5a, Hoxd12, and Cdx2 are necessary to pattern the intestines in other animals including, mice, chick and human. We have cloned these genes from the skate and are characterizing their expression by RNA whole mount in situ hybridization in the developing spiral intestine. The results will allow us to generate a profile of the conserved genes involved in intestinal differentiation. By comparing gene expression profiles among different vertebrates, we can link information at the molecular level with the structural and functional adaptations that have evolved in the digestive tracts across lineages. Therefore, the study of differential gene expression in embryonic development can provide an opportunity to understand events of vertebrate evolution dating back 400 million years.