The morphogenesis of ectodermal organs is regulated by epithelial mesenchymal interactions mediated by conserved signaling molecules. Analyzing the roles of these molecules will increase our understanding of mechanisms regulating organogenesis, and organ culture methods provide powerful tools in this context. Here we present two organ culture methods for skin and tooth development: the hanging drop method for the short-term culture of small explants and the Trowell-type method for the long-term cultures of variable size explants. The latter allows manipulations such as combining separated epithelial and mesenchymal tissues and the use of signal-releasing beads. The effects of signaling molecules on morphogenesis can be observed during culture by using tissues from GFP-reporter mice. After culture, the effects of signals on gene expression can be analyzed by in situ hybridization or quantitative RT-PCR.