Examination of genetic polymorphism of the transcription factor-encoding gene E2A in laboratory and wild mice by Southern blotting has revealed the presence of two alleles. The most frequent allele is found in Mus musculus (Mm) musculus, as well. as Mm domesticus. The less common allele is restricted to the Mm domesticus subspecies. Characterisation of these alleles has shown that the less common allele contains a deletion of approx. 500 bp located within a 1.8-kb intron immediately upstream from the E12 basic helix-loop-helix exon. DNA sequencing determined the deletion to span 536 bp including nucleotides 1045-1580 of the intron within the common allele. The deleted region includes several sequences with similarity to gene regulatory motifs; however, expression of E12 and intron splicing appear unaltered. The occurrence of an identical deletion in mice from different geographical regions suggests that the uncommon allele may have a long evolutionary history.