We established the Hirosaki small-eye rat (HiSER), which have small, opaque eyes transmitted in an autosomal recessive manner, from our stock of Sprague-Dawley rats (SDRs). HiSERs show massive and progressive disorganization of the eye structures, including disruption and involution of the lens and detachment and aggregation of the retina. Rudimentary ciliary muscle and inflammatory cell infiltration in the vitreous are also observed. In HiSERs, the last three exons (exons 4-6) of the Cryba1 gene, encoding betaA3/A1-crystallin on chromosome 10, is deleted. As a consequence, the Nufip2 gene, located downstream of the Cryba1 gene in the opposite direction, is juxtaposed to exon 3 of the Cryba1 gene. In HiSER eyes, a chimeric transcript is expressed containing exons 1-3 of the Cryba1 gene and a sequence derived from the 3’UTR of the Nufip2 gene. Irrespective of the presence of the chimeric transcript, neither mutant nor normal betaA3/A1-crystallin proteins are detected in HiSER eyes. On the other hand, the expression level of the Nufip2 gene is decreased in HiSER eyes. Because it is known that betaA3/A1-crystallin is expressed in the lens and retina, and the Nufip2 gene is expressed in the central nervous system, it is hypothesized that the disappearance of betaA3/A1-crystallin and, in addition, downregulation of the Nufip2 gene are causal reasons of the HiSER phenotype. So far, several animals with functional disruption of betaA3/A1-crystallin and, in humans, cataract patients with mutation of the Cryba1 gene, have been reported. In addition to these familiar phenotypes observed in both animal models and patients, HiSERs exhibit unique characteristics presumably due to its distinct genotype. HiSERs may provide a good opportunity for investigation of the functional roles of Cryba1 and Nufip2 in ocular development, and may become a useful animal model of lens and retinal degenerative disorders.