The existence of a murine homologue of the major basic protein (MBP) found in human eosinophil granules was initially hypothesized from structural similarities at the electron microscopic level. The results presented in this study have extended these observations by describing the identification/purification of a mouse MBP (mMBP) and the cloning of the gene encoding this eosinophil granule protein. Using protein purification methodologies with extravascular eosinophils, an mMBP homologue has been identified on the basis of strong (64%) N-terminal sequence homology with the mature human MBP (hMBP). Since hMBP results from a proteolytic cleavage of a precursor molecule, this sequence conservation suggests that the mouse granule protein is processed by a similar mechanism. The gene encoding mMBP was isolated using a hMBP cDNA clone as a heterologous probe in low criteria screens of mouse genomic and cDNA libraries. The genomic structure and nucleotide sequence of the mMBP exons are well conserved with the human gene, although homology alignments of the encoded proteins show that extensive sequence conservation occurs only in the mature portion of the MBP molecules. Expression data demonstrate that this gene is transcriptionally active in tissues containing eosinophil progenitor cells, such as femoral bone marrow. Genomic Southern blots using the mMBP gene at reduced stringency reveal the potential existence of a second, more divergent MBP-like sequence in the mouse. This suggests that, as with guinea pigs, the mouse genome may also encode the eosinophil major basic protein from more than one gene.