Deformed (Dfd), a homeotic selector gene required for segment identity in the head, and the Broad-Complex (BR-C), a steroid hormone-regulated locus required for metamorphosis of the epidermis and multiple internal tissues, are members of distinct genetic regulatory hierarchies. Their protein products contain DNA-binding domains (of the homeodomain and zinc-finger variety, respectively) and are believed to act by regulating the transcription of target genes. In this study we demonstrate that Dfd and BR-C mutants dying during metamorphosis share defects of CNS reorganization, ventral adult head development, and adult salivary gland morphogenesis. Specifically, the shared phenotypes are (i) failure to separate the subesophageal ganglion (SEG) from the thoracic ganglion (TG); (ii) structural and functional abnormalities of the proboscis and maxillary palps, innervated by the SEG; and (iii) failure of the adult salivary glands to extend into the thorax. Experiments performed with a conditional allele demonstrate that Dfd+ function during either larval life or metamorphosis is sufficient to rescue the SEG-TG separation phenotype. BR-C;Dfd double mutants show synergistic enhancement of the ventral head defects. This genetic interaction suggests that the segment identity and steroid hormone-sensitive regulatory hierarchies intersect during postembryonic development.