We describe the cloning and characterization of a novel rat gene, bwd (brain-enriched WD), which encodes a protein with four copies of the WD amino acid motif, suggesting involvement in protein-protein interaction and a regulatory function in the cell. Northern analysis reveals two size classes of mRNA (1.8 and 2.2 kb), expressed in many adult tissues and developmental stages. Expression is highest in brain, where the longer of the two RNAs predominates. cDNA sequences show that both RNAs encode the identical protein, differing only in their 3' untranslated regions, where the longer transcript contains two RNA instability signals (AUUUA). In situ hybridization to bwd RNA in adult brain shows a highly restricted pattern, localizing expression mainly to the Purkinje and granule neurons of the cerebellum, the pyramidal cells of the hippocampus, and the dentate gyrus. In cryosections of rat cerebellum and kidney, BWD is shown by immunohistochemistry to be localized in the nucleus and cytoplasm of cerebellar Purkinje and granule neurons, and in predominantly the cytoplasm of cells surrounding kidney ducts. Taken together, these results suggest a specialized function for BWD in the brain. Sequence similarity comparisons with bwd reveal structural homologs of unknown function in human, mouse, Drosophila, Arabidopsis and C. elegans, and provide evidence that this set of sequences forms a new subfamily of WD-repeat genes. By sequence comparisons with expressed sequence tags (ESTs), the human homolog of bwd is predicted to reside in the chromosome 1q12-23 region, where several genetic diseases are known to map.