The autosomal-recessive mutation hydrocephalus3 (hy3) results in lethal communicating hydrocephalus with perinatal onset. We recently described a hydrocephalus-inducing transgenic insertional mutation, OVE459, which represents a new allele of hy3. Direct cDNA selection performed on a wild-type mouse BAC clone spanning the OVE459 insertion locus on chromosome 8 led to the identification of two novel candidate genes, Hydin and Vac14. The transgene insertion resulted in a rearrangement of Hydin exons in OVE459 mice. Hydin consists of at least 86 exons spanning over 340 kb of genomic DNA. The full-length Hydin transcript is nearly 16 kb, encoding a putative 5099 amino acid protein. Northern analysis revealed a marked reduction of Hydin mRNA in both OVE459 and hy3 homozygotes relative to wild-type littermates. A single CG base-pair deletion in exon 15 of Hydin was discovered specifically in mice carrying the spontaneous hy3 mutant allele. This deletion creates a premature termination signal two codons downstream of the mutation, likely resulting in the loss of 89% of the full-length gene product. Within the neonatal brain, Hydin expression is confined to the ciliated ependymal cell layer lining the lateral, third and fourth ventricles. Other sites of Hydin expression include the ciliated epithelial cells lining the bronchi and oviduct, as well as in the developing spermatocytes in the testis. The Hydin gene product is not closely related to any previously identified protein, with the exception of a 314 amino acid domain with homology to caldesmon, an actin-binding protein, suggesting an interaction with the cytoskeleton.