During development of the chick brain stem, cranial motor neuron subpopulations differentiate at distinct axial levels and extend their axons along specific pathways into the periphery. Differences in phenotype and axonal trajectory of these neuronal populations might be governed by the expression of different repertoires of transcription factors. In 2- to 7-day chick embryos, we find that genes of the LIM homeobox family are expressed differentially among cranial motor nuclei. Whereas Islet-1 is expressed by motor neurons of all cranial nerves, Islet-2 is expressed only in nuclei that contain somatic motor neurons and transiently in a specialized population of contralateral vestibuloacoustic efferent neurons. Lim-3 is expressed in the hypoglossal and accessory abducens nuclei only, and Lim-1 and Lim-2 are not expressed by cranial motor neurons. Our findings are consistent with a role of these transcription factors in determining neuronal phenotype and axonal pathfinding.