Purkinje cell protein-2 (PCP2), also known as L7, is a member of the GoLoco protein family with highly cell-specific expression, being restricted to cerebellar Purkinje cells and retinal bipolar neurons in various species. However, its function in these tissues is unknown. Previous studies have suggested that PCP2 is a guanine nucleotide dissociation inhibitor, or a guanine nucleotide exchange factor. The Pcp2 gene is known to have many splice variants in both cerebellar Purkinje cells and retinal bipolar neurons. Here, we tested the hypothesis that a novel Pcp2 splice variant is conserved in closely related laboratory rodents (mice, rats, and hamsters). After analyzing alternative splicing of this gene in the Purkinje cells and retinas of these rodent species, we confirmed the presence of the novel longer transcript in mice. However, assessment of Pcp2 transcripts using polymerase chain reaction amplification of complementary DNA revealed this long splice variant containing the additional exon 3B to be absent from rats and hamsters. Thus, the novel Pcp2 transcript is particular to mouse cerebellar Purkinje cells and retinal bipolar neurons. It is likely to have arisen in this species, as a result of spontaneous mutation or de novo rearrangements. This gene presumably serves a very specific and, as yet, unknown function in the eyes and/or Purkinje cells of mice.