Developmental Evolution (DE) contributes to various research programs in biology, such as the assessment of homology and the determination of the genetic architecture underlying species differences. The most distinctive contribution offered by DE to evolutionary biology, however, is the elucidation of the role of developmental mechanisms in the origin of evolutionary innovations. To date, explanations of evolutionary innovations have remained beyond the reach of classical evolutionary genetics, because such explanations require detailed information on the function of genes and the emergent developmental dynamics of their interactions with other genetic factors. We argue that this area has the potential to become the core of DE's disciplinary identity. The main challenge in developing a research program for DE along these lines, however, is to provide a methodological framework that accounts for the fact that developmental mechanisms continue to evolve after a character has originated. Developmental mechanisms elucidated in a derived species may therefore not provide insights into the evolutionary origin of the character in question. To meet this challenge, we propose a set of questions that may guide us in our search for valid inferences on the role of developmental mechanisms in the explanation of evolutionary innovations.