Chronic granulomatous disease is an inherited disease characterized by the inability of phagocytes to generate normal amounts of superoxide, leaving patients susceptible to opportunistic, life-threatening infections. In the majority of cases, cytochrome b 558 is absent in the X-chromosomal form of CGD. However, the neutrophils from six of nine X-linked CGD patients, reported here, expressed normal or decreased amounts of this cytochrome and are referred to as "variant" forms. In three of these six variant patients, a roughly proportional decrease in cytochrome b 558 expression and production of H 2 O 2 were found. In two cases this phenotype could be well explained by special splice mutations, whereas in the third case it was caused by a missense mutation, predicting Ser 193 → Phe. In the other three variant patients, cytochrome b 558 expression and H 2 O 2 production were clearly disproportionate as the generation of H 2 O 2 was much more decreased than cytochrome expression. Missense mutations also were found in these cases. One of these mutations, predicting Leu 546 → Pro and affecting the putative nicotinamide adenine dinucleotide phosphate binding site, led to normal levels of cytochrome b 558 expression and reduced H 2 O 2 production. In the other two mutations, predicting Pro 339 → His and His 338 → Tyr, the putative flavin adenine dinucleotide binding site was affected. This could explain the corresponding uncommon phenotypes, characterized by zero or trace amounts of H 2 O 2 production and the expression of relatively high amounts of nonfunctional or low functional cytochrome b 558 , respectively. The only missense mutation found that prevented the expression of any cytochrome b 558 was caused by a predicted His 222 → Arg exchange in one of the three classic cases. The two other classic phenotypes were caused by splice mutations.