The organization of embryonic efferent cranial nerves is addressed here by interspecies comparison of segmentally patterned neuromeres, efferent neuronal populations and early mesodermal sources of target muscles. The segmental constancy of these three structural patterns is evaluated for elasmobranch, teleost, reptile, bird and mammal embryos and compared with the segmentally restricted expression patterns of Hox genes. A conserved series of hindbrain neuroepithelial segments (rhombomeres) is present in all of these taxa. Dye-labeling experiments demonstrate that the segmental locations of efferent neurons projecting through individual cranial nerves are likewise highly conserved. Notable segmental variation is however shown in the location of the VI and IX-XII motoneurons, suggesting the likelihood of homeotic-like changes in relations between rhombomere and neuronal 'identity' during vertebrate evolution. Since experimentally induced shifts in expression borders of Hox genes appear to be correlated with alterations in segment identity and/or neuronal phenotype, the need for further examination of segmental locations of specific neuronal groups and the segmental expression patterns of Hox genes between species is emphasized. Comparison of early cranial mesodermal subdivisions in elasmobranchs with descriptions of somitomeres in amniotes suggests that a series of axially unique mesodermal populations may also be conserved throughout vertebrates. The possibility is raised that common mechanisms of axial specification may underlie the initial appearance of segmental patterning in both neural and mesodermal layers during gastrulation. Implications of these conserved patterns for understanding the phylogenetic origin of the vertebrate head are briefly discussed.