New advances in developmental genetics are providing a bridge to connect the study of development and evolution. The successful integration of these fields, however, is dependent on having a clear understanding of the concept of homology. Therefore, developmental genetic data must be placed within the context of the comparative method to provide insight into the evolutionary and developmental origins of traits. The comparative analysis of traits derived from several hierarchical levels (genes, gene expression patterns, embryonic origins and morphology) can potentially reveal scenarios of developmental integration, opportunity and constraint. Moreover, this approach has implications for resolving modern controversies surrounding the concept of homology.