Myeloperoxidase (MPO), present in the azurophilic granules of polymorphonuclear leukocytes, is a myeloid enzyme whose synthesis is restricted to promyelocytes. Complete hereditary MPO deficiency affects 1 in 2,000 to 4,000 individuals; however, the genetic cause of this defect is unclear. We have determined the molecular basis of MPO deficiency in one individual (SQ). Granulocytes of SQ had no MPO activity, and had complete absence of mature and precursor MPO protein by Western blotting. Scanning MPO gene structure by Southern blotting detected a novel BgI II fragment in SQ; no other alteration in gross gene structure was detected. We hypothesized that a single base pair mutation formed a new BgI II restriction site, and that this occurred in exon 10 of MPO gene. As predicted, exon 10 from SQ was cleaved by BgI II, but DNA from the normal patients and five other MPO-deficient patients was not cleaved by this enzyme. Direct sequencing of the polymerase chain reaction (PCR) product of exon 10 showed a C to T substitution at codon 569 in exon 10, resulting in arginine (CGG) to tryptophan (TGG) substitution and creating a novel BgI II site. The mutation was homozygous, as shown by both sequencing and Southern blotting, and no other alterations in base sequence were detected. To determine the frequency of this mutation, DNA was collected from 400 normal individuals, and the presence of the mutation was examined by digesting with BgI II after amplifying exon 10 by PCR. No other case with the novel BgI II site was detected, suggesting that this is not a restriction fragment length polymorphism. The rest of the coding region of the MPO gene was sequenced in DNA from SQ, as well as from the five other MPO-deficient individuals and one normal person; no other mutations were found. Our results suggest that a point mutation at codon 569 of MPO gene represents one molecular form of MPO deficiency.