The Pax-6 transcription-factor gene, containing a paired domain and a paired-type homeodomain, is conserved in structure and ubiquitously present among Metazoa(1-5). It is required for development of the central nervous system, and is mutated in human aniridia, mouse and rat small eye and Drosophila eyeless(6). We identified the Pax-6 gene of the nematode Caenorhabditis elegans in genetic studies of male tail morphology(7,8). C. elegans Pax-6 encodes at least two independent genetic functions. One, like other Pax-6 genes, contains paired and homeodomains; this constitutes the genetic locus vab-3 (ref. 9). The other, described here, is expressed from an internal promoter and contains only the homeodomain portion; this constitutes the genetic locus mab-18 (ref. 7), The mab-18 form of the gene is expressed in a peripheral sense organ and is necessary for specification of sense-organ identity. Its function in this context could be to regulate the expression of cell recognition and adhesion proteins required for sense-organ assembly.