Homeobox-containing genes are thought to perform essential functions in the process of pattern formation in vertebrates and invertebrates. They provide cells with positional information critical for normal embryonic development. Since most of the identified homeobox genes in Xenopus seem to provide positional information for the development of the trunk, we have concentrated on genes that may be specifically involved in the formation of the head region. Using a polymerase chain reaction strategy we have searched for Xenopus homeobox-containing genes that might provide positional cues for correct development of the brain. In this paper we report the identification and cloning of a novel gene that by homology appears to be a member of the Distal-less homeobox gene family. We show that its temporal expression patterns in the cement gland, neural crest derived visceral arches, retina and forebrain, while quite diverse, does suggest shared developmental features which may be required for correct craniofacial development and the regionalization of the Xenopus brain. Furthermore, expression of this gene at later stages is primarily restricted to the tadpole forebrain suggesting that the Distal-less gene product continues to play a role after the initial brain patterning is complete.