A comparison of the brains of lampreys and hagfishes is carried out in an attempt to reconstruct the anatomy of the brain of the last common ancestor of craniates: i.e., the morphotype of the craniate brain. This brain consisted of tel-, di-, mes-, and rhombencephalic divisions; the presence of a metencephalic/cerebellar division is questionable. All major sensory and motor systems (with the possible exception of the oculomotor system) that are typical of craniates were present in the morphotype. There were extensive bilateral secondary olfactory projections to the telencephalic pallium, as well as bilateral retinofugal projections to diencephalic, pretectal, and tectal targets. The rhombencephalon was subdivided into dorsal (viscero- and somatosensory) and ventral (branchiomotor) zones. The spinal cord projected to most rhomb- and mesencephalic areas; in turn, it received descending projections from the mes- and rhombencephalic reticular formation and from the octaval nuclei. The reconstruction of such a morphotype depends on the recognition of characters that are plesiomorphic for craniates, as determined by comparative, cladistic analysis. In many cases (gross morphological, topological and cytoarchitectural characters), such an analysis cannot be carried out, because characters that appear as discrete entities in one taxon are lacking or difficult to delineate from other characters in other taxa. The distribution of these characters in lampreys and hagfishes, and the developmental mechanisms that brought them about, offer a challenging problem in evolutionary neurobiology.