Our knowledge of the evolution of gene regulation is still rudimentary. From the few well-studied paradigms, it is apparent that regulatory systems are diverse and complex. Consequently, broad generalizations should not be made at this time. Rather, detailed molecular, developmental, and phylogenetic data are needed to elucidate simultaneously the molecular mechanisms and evolution of gene regulation for a number of genes and species. An added complication of such studies is that the regulatory properties of a gene evolve somewhat independently of gene function. Thus, functional information cannot be used reliably to infer regulatory properties, and vice versa. Once the difficult task of identifying regulatory elements and their role in evolution has been achieved, determining the mutational events underlying the evolution of specific elements can proceed by the comparative method.