Previous studies identified the gene encoding the erythrocyte membrane protein 4.2 (Epb4.2) as a candidate for the mouse mutation pallid (pa); Epb4.2 genetically colocalized near pa on mouse Chromosome 2, and a truncated Epb4.2 transcript was present in tissues derived from pallid mice. We report here evidence that Epb4.2 and pa are not allelic. The pallid cDNA and intron/exon boundaries show no significant variation from the known BALB/c and C57BL/6J Epb4.2 sequence, and normal immunoreactive 72-kDa protein 4.2 is present in pallid tissues. Two recombinations between Epb4.2 and pa were identified in 173 phenotypically mutant (C57BL/6J-pa/pa x Mus castaneus) F2 animals. Northern blotting reveals a truncated Epb4.2 transcript in kidney mRNA from normal wild Mus domesticus (WSB/Ei) mice that comigrates with the pallid Epb4.2 mRNA. As the pa mutation originally arose in a wild M. domesticus mouse, we conclude that the Epb4.2 mRNA characteristic of pallid is a normal polymorphism derived from its wild ancestor and that Epb4.2 and pa are distinct loci.