Here we describe and compare the expression patterns of the murine genes Lhx2 and Msx1 and their Drosophila orthologues apterous (ap) and muscle-segment homeobox (msh). We find that Lhx2 and Msx1 show complementary patterns of expression in most tissues including the neural and cranial epithelium, pituitary gland, olfactory organs, and neural tube; in contrast, Lhx2 and Msx1 are coexpressed in the developing limbs. Strikingly, the spatial relationship between ap and msh expression in Drosophila is very reminiscent of the expression of their murine orthologues. ap and msh show complementary expression in the leg and antennal imaginal discs, brain and ventral ganglion of the central nervous system (CNS), but both are coexpressed in the wing imaginal disc. These observations suggest conservation in the regulation of these genes between Drosophila and mice.