A rat strain with congenital nuclear cataracts has been established. Segregation analyses indicated that this phenotype had an autosomal recessive mode of inheritance, implying that a loss of function mutation of a single autosomal gene was responsible. The gene was mapped to the D15Rat6 locus on chromosome 15 through a linkage analysis using 93 backcrossed rats. The connexin 46 gene (Gja3) was found to be located close to the locus, and was regarded as a strong candidate because of its pivotal role in the lens fiber cells. Expression of the gene in the lens was comparable between the cataract and control rats when evaluated with immunohistochemistry and reverse transcription-polymerase chain reaction. However, a non-conservative missense mutation, Glu42Lys, was found in the gene of the cataract rats, which was likely to be responsible for the pathogenesis. This strain will be useful in pathophysiological studies on nuclear cataracts.