Background: An uncommon inherited primary immunodeficiency illness (PID) known as chronic granulomatous disease (CGD) is characterised by an increased vulnerability to serious bacterial and fungal infections. It results from defects in one of the five polypeptide subunits of the nicotinamide adenine dinucleotide phosphate-oxidase (NADPH) oxidase complex, CYBB (gp91-phox), NCF1 (p47-phox), CYBA (p22-phox), NCF2 (p67-phox), or NCF4 (p40-phox) with a resulting failure of the phagocytes in generating a variety of microbicidal reactive oxygen radicals during respiratory burst. Objective: In the present study we aimed to diagnose AR-type of CGD by detection of NCF-2 gene expression using real time RT-PCR as a cheaper diagnostic method for CGD subtypes categorization among CGD children. Patients and methods: This case-control study was conducted on 15 children provisionally diagnosed as CGD patients with dihydrorhodamine (DHR) stimulation index (Group I). The study also included 12 mothers and 8 fathers of the studied patients (Group IIa and IIb respectively) to detect the genetic mutations in carriers, if any, and 14 apparently healthy children as a control group (Group III). Results: In the present study, cases with a fold change of NCF-2 gene expression less than 0.67 were considered defective for NCF-2 gene expression. At this cut-off value, from our molecularly studied subjects, 2 CGD cases and one mother showed under-expression of NCF-2 gene. Conclusion: We could establish the diagnosis of 2 out of 15 CGD cases as AR- CGD form, derived from defects in the NCF-2 gene, which encodes gp67-phox of the oxidase, without the need to use complex and expensive methodologies such as northern blot, or genomic DNA sequencing.