Myeloperoxidase and eosinophil peroxidase were separated and purified from rat bone marrow cells using cetyltrimethylammonium bromide as the solubilizer and then with column chromatographies on CM-Sephadex C-50 and Con A-Sepharose. Both purified enzymes were observed to be apparently homogeneous by SDS-polyacrylamide gel electrophoresis. Myeloperoxidase consisted of two subunits of Mr 57,000 and 15,000, and eosinophil peroxidase two of 53,000 and 14,000. On structural analysis of the enzymes, their visual and ESR spectra revealed that the structure surrounding the heme in myeloperoxidase was different from that in eosinophil peroxidase. Moreover, substrate specificity and sensitivity to inhibitors such as azide and cyanide differed between the two enzymes. Rat bone marrow possesses two distinct peroxidases, myeloperoxidase and eosinophil peroxidase, which have different subunits and different heme microenvironments. Therefore, the difference in enzymatic function between the two peroxidases may be due to their structures.