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Chronic granulomatous disease (CGD) is a rare primary immunodeficiency disease characterized by recurrent bacterial and fungal infections and is due to impaired function of superoxide-producing nicotinamide adenine dinucleotide phosphate oxidase. Patients may have elevated serum IgE levels mainly because of a high incidence of sensitization to Aspergillus species. In addition to a predisposition to infections, patients with CGD might have hyperinflammation presenting itself as chronic inflammatory lesions involving gastrointestinal mucosa, skin, lungs, eyes, and brain. Here, we present a case that mainly presented with chronic gingivitis and very high serum IgE levels and had been referred to our hospital with a probable diagnosis of hyper-IgE syndrome, another congenital immunodeficiency that is also characterized by increased susceptibility to bacterial or fungal infections and very high serum IgE levels. Detailed history of the patient revealed recurrent upper and lower respiratory tract and skin infections. He was diagnosed as having CGD by documenting defective phagocyte superoxide production and the diagnosis was then confirmed by mutation analysis. Family screening revealed that a younger brother was also affected. CGD should be considered in the differential diagnosis of patients with recurrent infections, chronic inflammatory lesions, and high serum IgE levels. These cases emphasize the importance of detailed history taking for diagnosis and family screening for identification of other affected members.