Chronic granulomatous disease (CGD) is a primary immunodeficiency caused by mutations of the phagocytic nicotinamide adenine dinucleotide phosphate (NADPH) oxidase. Autosomal recessive p47 -deficient CGD (p47 CGD) is the second most frequent form of the disease in western countries, and more than 94% of patients have a disease-causing dinucleotide deletion (ΔGT) in the neutrophil cytosolic factor 1 () gene. The ΔGT mutation is most likely transferred onto the from one of its two pseudogenes co-localized on the same chromosome. The presence of pseudogenes in healthy individuals makes the genetic diagnostics of ΔGT p47 CGD challenging, as it requires the distinction between ΔGT in and in the two pseudogenes. We have developed a diagnostic tool for the identification of p47 CGD based on PCR co-amplification of and its pseudogenes, followed by band intensity quantification of restriction fragment length polymorphism products. The single-day, reliable p47 CGD diagnostics allow for robust discrimination of homozygous ΔGT p47 CGD patients from heterozygous carriers and healthy individuals, as well as for monitoring gene therapy efficacy.