Background Chronic granulomatous disease (CGD) is a primary immunodeficiency resulting from the absence or malfunction of oxidative mechanism in phagocytic cells. The disease is due to a mutation in one of four genes that encode subunits of the nicotinamide adenine dinucleotide phosphate (NADPH) oxidase complex. Affected patients experience severe infections and granuloma formation due to exuberant inflammatory responses. Some evidence suggests that eosinophilic cystitis (EC) is included in the spectrum of inflammatory manifestations. EC is an inflammatory disease, rare in childhood, which may require different, nonstandardized therapeutic approaches, ranging from antihistamines to cyclosporine.Case-Diagnosis/Treatment Herein we describe the cases of two CGD patients with CGD who experienced EC during hospitalization for a severe infection. Conclusions EC in immunocompetent children seems to have a self-limiting course, unlike in CGD patients, in whom it presents a prolonged and recurrent course. We focus on the effective therapy administered to our patients with CGD and review the corresponding literature.