Rats homozygous for the spontaneous cerebellar vermis defect mutation (cvd) or hobble mutation (hob) exhibit cerebellar and midbrain defects, possibly as a result of abnormal neuronal migration. Both mutant rats demonstrate laminar structure abnormalities in the fused cerebellar hemispheres and ectopic cerebellar tissues in the cerebello-pontine junction. Previous genetic studies showed that cvd and hob were allelic and suggested that Unc5h3, the causative gene of the mouse rostral cerebellar malformation (rcm) mutation, was a strong candidate for both cvd and hob. Unc5h3 encodes a receptor mediating the repulsive action for Netrin-1 and has an important role during cell migration in the developing murine cerebellum. Here, we describe positional candidate cloning of cvd and hob, and identified cvd and hob mutations in the rat Unc5h3. The cvd mutation is a nucleotide conversion of G to T resulting in a premature termination at codon 451 of the UNC5H3 protein. The hob mutation is a 2-bp insertion resulting in a frame shift from codon 312 and a premature termination at codon 385 of the UNC5H3 protein. Both cvd and hob mutations are predicted to lead to truncated UNC5H3 proteins lacking their cytoplasmic region required for Netrin-Unc5h3 signaling pathway. Therefore, we conclude that Unc5h3 is causative gene of both cvd and hob mutant phenotypes. Rats homozygous for Unc5h3cvd or Unc5h3hob are the first mammalian Unc5h3 mutant model other than Unc5h3rcm/rcm mice, and will provide a useful tool for further understanding of the biological function of Unc5h3.