Major basic protein and eosinophil peroxidase are predominant cationic proteins in the cytoplasmic granules of human eosinophilic leukocytes. Each of these proteins has been purified, and major basic protein and the lower molecular weight subunit of eosinophil peroxidase have been found to comigrate on polyacrylamide gel electrophoresis in sodium dodecyl sulfate with similar apparent molecular weights of about 14,700. Because previous molecular weight estimates for these proteins have not recognized the similar molecular weights of these two cationic eosinophil granule constituents, we have evaluated the possible relatedness of these proteins. Upon protein sequence analyses, it was found that the N-terminal 20 amino acid residues of each of these two purified polypeptides differed. These findings established that major basic protein and the smaller subunit of eosinophil peroxidase, although of comparable molecular weights, are two distinct proteins within the cytoplasmic granules of human eosinophils.