Myeloperoxidase from human neutrophils was isolated by ion-exchange and gel-filtration chromatography and shown by SDS-polyacrylamide gel electrophoresis to be comprised of alpha and beta subunits with apparent Mr values of 58,000 and 15,000, respectively. The apparent Mr of the native protein was 130,000-140,000, indicating that the holoenzyme has the quaternary structure alpha 2 beta 2. Automated Edman degradation of the separated alpha and beta subunits showed that the amino-terminal sequences were different from one another and demonstrated no sequence microheterogeneity. Comparison of these sequences with those in the National Biomedical Research Foundation data bank of protein sequences revealed that the subunits of human myeloperoxidase were not homologous to any known protein. Myeloperoxidase purified from HL-60 cells grown in culture demonstrated the same alpha 2 beta 2 subunit structure. Three isoenzymes of myeloperoxidase, prepared by gradient elution from a CM-Sepharose column, underwent quantitative analysis. No structural basis for the different elution pattern of the myeloperoxidase isoenzymes was discerned by amino-acid analysis, N-terminal sequence, polyacrylamide gel electrophoresis, or digestion with neuraminidase or enzymes known to cleave N-linked heterosaccharides. The structural basis for the myeloperoxidase isoenzymes of human neutrophils, each possessing equivalent activity, is not apparent from these studies.