A growing body of evidence suggests that changes in transcriptional regulation form an important part of the genetic basis for the evolution of development. At a microevolutionary level, all the necessary conditions are present: populations harbor abundant genetic variation for differences in transcription profiles, a substantial fraction of these variants can influence organismal phenotype, and some variants have fitness consequences and are subject to natural selection. At a macroevolutionary level, the evidence is less direct but strongly suggestive: specific differences in anatomy and gene expression are often correlated, while comparisons of transcription profiles among distantly related taxa point to extensive evolutionary changes in regulatory gene networks. Understanding how transcriptional regulatory systems evolve, and what contributions these changes have made to the evolution of phenotype, represents a major challenge for Evo-Devo.