ICR-derived retinal dysfunction (IRD) 1 and IRD2 mice are new spontaneous mouse models of rod-cone and rod dysfunctions, respectively. In this study, we investigated the cause of rod dysfunction in IRD1 and IRD2 mice. Gene expression of rod phototransduction proteins was analyzed by quantitative real-time RT-PCR. mRNA levels of Gnat1, which encodes the alpha subunit of rod transducin (Tralpha), were severely reduced. Tralpha protein was immunohistochemically undetectable in both IRD1 and IRD2 mice. Sequencing of Tralpha cDNA revealed a 48-base pair (bp) insertion between exons 4 and 5 in both mutant strains. The insertion changed codon 150 (TAC) to a stop codon (TAG) (Tyr150Ter). The truncated Tralpha protein was undetectable in the retinas of both mutants by western blot analysis using a primary antibody against the N-terminal region. A 57-bp deletion was identified in intron 4 of the Gnat1 gene, which encodes the Tralpha protein, and included the last two bases of the splice donor site of intron 4. Thus our results showed that IRD1 and IRD2 mice harbor a nonsense mutation in the Gnat1 gene, resulting in the absence or suppressed expression of the Tralpha protein, which is the likely cause of rod dysfunction in both mutants.