Three mouse genes, Gli, Gli-2, and Gli-3, which share a similar zinc finger domain with the products of the Drosophila segment polarity gene cubitus interruptus and the Caenorhabditis elegans sex-determining gene tra-1 were cloned and characterized. The expression patterns during postimplantation development of the three genes were analyzed by Northern blot, whole-mount, and section in situ hybridizations. Expression was first detected during gastrulation in both the ectoderm and mesoderm. Later in development, their expression became more restricted in various ectoderm- and mesoderm-derived tissues and was not detectable after completion of organogenesis. Interestingly, in the developing neural tube, Gli showed a narrow ventral domain of expression, whereas Gli-2 and Gli-3 showed a broad and dorsally restricted domain. Expression of these three Gli genes in various ectoderm- and mesoderm-derived tissues suggests that they play multiple roles during postimplantation development. Consistent with this hypothesis, a naturally occurring Gli-3 mutation, the mouse extra-toes mutant; shows defects in both mesoderm- and ectoderm-derived tissues.