Introduction : Chronic granulomatous disease (CGD) is an inherited disorder of the NADPH oxidase characterized by severe bacterial and fungal infections and excessive inflammation. CGD is caused by a defect in the burst of oxygen consumption that normally accompanies phagocytosis in myeloid cells. The enzyme that catalyzes the respiratory burst, the leukocyte NADPH oxidase, consists of subunits, four of which are important for CGD:gp91phox (or Nox2) and p22phox, located in membranes, as well as two cytosolic oxidase components, p47phox and p67phox. CGD is caused by a defect in any of these four components. Aim of work : The aim is to identify the defective proteins implicated in the pathogenesis of the CGD in Egyptian families, to study the mode of inheritance in such families. Subjects and methods : Our study included 28 CGD patients (15 males and13 females) with ages ranging from 2 months to 14 years. Patients with CGD diagnosed by DHR test (dihydrorhodamine) together with the clinical picture of the disease. Anticoagulated (EDTA) samples were stained and analyzed by flow cytometry. Results :Our study revealed deficiency in P22phox in 13 patients (46.4%) followed by P47phox in 9 patients (32.1%), gp91phox in 4 patients (14.3%) and P67phox in 2 patients (7.1%). Conclusion :In countries with limited resources and yet large number of CGD patients like Egypt, the analysis of the defective proteins by flow cytometry will be the optimum solution for confirming the diagnosis, especially in laboratories that carry the DHR test and are already equipped with flow cytometry.