Recently, clinicians and scientists have focused on tissue engineering for regenerative medical therapy. This approach promises to provide remarkable clinical breakthroughs for the future. In oral and craniofacial medicine, most scientific approaches to tissue engineering currently involve tooth and bone, while little progress has been made toward regenerating organs such as salivary gland. To develop strategies for salivary gland regeneration, it will be important to understand the molecular mechanisms of normal salivary development. This mini-review describes a recently developed and tested set of approaches for identifying and characterizing molecules essential for branching morphogenesis and other developmental processes. It shows the value of using laser microdissection and the new process of T7-SAGE for gene discovery of putative candidate molecules that may be crucial regulators or mediators. We describe a stepwise series of associated strategies for reliable identification and functional testing of a candidate molecule, as well as its successful application to a specific candidate molecule originally identified by T7-SAGE.