Mutations in the gene encoding the zinc finger transcription factor TRPS1 result in tricho-rhino-phalangeal syndrome, characterized by craniofacial and skeletal abnormalities, and sparse scalp hair. In this study, Trps1 was identified by microarray hybridization analysis as having a complex pattern of spatiotemporal regulation in murine skin during morphogenesis. During early skin development, Trps1 expression decreased in the epidermis while simultaneously increasing in the dermis. Trps1 was specifically expressed in the nuclei of mesenchymal cells during hair follicle morphogenesis. An analysis of Trps1 expression during postnatal murine hair follicle cycling revealed that the protein localized to the nuclei of dermal papillae cells during telogen and anagen. Additionally, we found that Trps1 consistently localized to the nuclei of dermal papillae cells and the highly proliferative epithelial cells of mouse, rat and human hair follicles.