Chronic granulomatous disease (CGD) is a rare congenital disorder in which phagocytes cannot generate superoxide (O(2)(-)) and other microbicidal oxidants because of mutations in one of the four components of the O(2)(-)-generating NADPH oxidase complex. A subgroup (approximately 5% of identified CGD patients) has been reported to have mutations in the gene encoding the small p22 phox subunit of the flavocytochrome b (558), the redox element of phagocyte NADPH oxidase. Here, we report the case of an autosomal recessive CGD patient with a defect in the p22 phox subunit. Neutrophils failed to produce O(2)(-) in response to soluble and particulate stimuli, and cytochrome b (558) was absent as measured by immunoblotting and difference absorption spectra. Mutations in the p22 phox mRNA of the patient were detected by reverse transcription/polymerase chain reaction amplification and sequencing. The defect in the mRNA was a 179-bp insertion associated with a 21-bp deletion of the beginning of exon 5 at position 315 from the translation start codon of the p22 phox cDNA. This defect was also detected in the patient's parents. In the genomic DNA of the patient, the molecular defect was a homozygous 36-bp deletion in the linking sequence between intron 4 and exon 5. This genomic deletion corresponded to 15 bp of the 3' extremity of intron 4 and 21 bp of the beginning of exon 5 (the same deletion of exon 5 seen in the corresponding mRNA). The splicing mRNA error is attributable to the loss of the ag acceptor site of intron 4 and the utilization of a cryptic splice site with an ag sequence at position 355-356 of intron 4.