Among the bilateral animals, a centralized nervous system is found in both the deuterostome and protostome. To address the question of whether the CNS was derived from a common ancestor of deuterostomes and protostomes, it is essential to know kinds of genes existed in the CNS of the putative common ancestor and to trace the evolutionary divergence of genes expressed in the CNS. To answer these questions, we took a comparative approach using different species, particularly focusing on one of the lower bilateral animals, the planarian (Platyhelminthes, Tricladida), which is known to possess a CNS. We determined the nucleotide sequence of ESTs from the head portion of planarians, obtaining 3,101 nonredundant EST clones. As a result of homology searches, we found that 116 clones had significant similarity to known genes related to the nervous system. Here, we compared these 116 planarian EST clones with all ORFs of the complete genome sequences of the human, fruit fly, and nematode, and showed that >95% of these 116 nervous system-related genes, including genes involved in brain or neural morphogenesis, were commonly shared among these organisms, thus providing evidence at the molecular level for the existence of a common ancestral CNS. Interestingly, we found that Ϸ30% of planarian nervous system-related genes had homologous sequences in Arabidopsis and yeast, which do not possess a nervous system. This implies that the origin of nervous system-related genes greatly predated the emergence of the nervous system, and that these genes might have been recruited toward the nervous system. F or understanding the evolutionary divergence of metazoans, the CNS is a key organ because of its highly organized developmental patterning system. Comparative studies of the CNS should yield valuable insights into its evolutionary history. Among bilateral animals, although both of deuterostomes and protostomes possess a centralized nervous system (1), comparative embryology has suggested that their CNSs should have arisen from different origins, because the deuterostome CNS is formed from the dorsal neural tube, whereas that of protostomes develops from the ventral ectoderm (2). Recently discovered molecular evidence, however, has provided support for the opposite conclusion in this longstanding problem of evolutionary morphology, namely the conserved expression patterns of many regulatory genes (3). To answer the question of whether both of these types of CNS were derived from a common ancestor, it is essential to gain more extensive knowledge of genes in the CNS of more basal groups of bilaterians and to compare these genes with those of other organisms.Planarians (Platyhelminthes, Tricladida) possess a CNS with a simple, primitive morphology (4, 5). The planarian CNS is composed of the cephalic ganglion and a pair of ventral nerve cords. The cephalic ganglion forms an inverted U-shaped structure with nine branches connecting to the sensory organs on each side (6, 7). The planarian cephalic ganglion exhibits many morphological fea...