Chronic granulomatous disease (CGD) is a primary immunodeficiency caused by defects in any one of 4 genes encoding phagocyte NADPH oxidase subunits. Unlike other CGD subtypes, in which there is great heterogeneity among mutations, 97% of affected alleles in patients previously reported with A47 0 CGD carry a single mutation, a GT deletion (⌬GT) in exon 2 of the p47-phox gene, NCF-1. This unusually high incidence results from recombination events between NCF-1 and its highly homologous pseudogenes, in which ⌬GT originates. In 50 consecutive patients with A47 0 CGD, 4 were identified who were heterozygous for ⌬GT in NCF-1, and for the first time, 2 were identified whose DNA appeared normal at this position. To avoid co-amplification of pseudogene sequence and to enable the identification of mutations in these patients, allele-specific polymerase chain reaction was used to amplify alleles not containing ⌬GT. In each of the 4 patients who were heterozygous for ⌬GT, an additional novel mutation was identified. These were 2 missense mutations, G125 3 A in exon 2 (predicting Arg42 3 Gln) and G784 3 A in exon 8 (Gly262 3 Ser), and 2 splice junction mutations at the 5 end of intron 1, gt 3 at and gtg 3 gtt. The first of 2 patients who appeared normal at the GT position was a compound heterozygote with the G125 3 A transition on one allele and a deletion of G811 on the other. In the second of these patients, only a single defect was detected, G574 3 A, which predicts Gly192 3 Ser but is likely to result in defective splicing because it represents the final nucleotide of exon 6. (Blood. 2001;97:305-311)