Background: Chronic granulomatous disease (CGD) is a rare primary immunodeficiency. Infections of the lungs, skin, lymph nodes, and liver are the hallmark of CGD with frequent initial manifestations of the disease. The aim of the present study was to describe the sites of infections and their causative agents in 38 CGD pediatric patients.Methods: This was a retrospective single-center cohort study comprising CGD patients, and followed for over last 40 years at the Allergy and Immunology Unit of a tertiary hospital in São Paulo, Brazil. Sites of infections and their causative agents were described.Results: A total of 38 patients were included (36 males and 2 females). Median age at the onset of symptoms was 45 days (7 days–7 years) and that at the time of diagnosis was 23 months (1 month–12 years); 31.6% of the parents reported death of relatives during childhood and 21% (8 cases) had another male family member with CDG. The most common infections were pneumonia (81.6%), skin infections (50.0%), adenitis (42.1%), and liver abscess (23.7%). In all, 188 cultures were positive (85.6% for bacteria and 14.4% for fungi). The most prevalent bacterial agents were Staphylococcus sp. (12.4%), Staphylococcus aureus (11.2%), and Klebsiella pneumoniae (9.3%). Aspergillus sp. and Candida sp. were 56% and 22.2% of the isolated fungi, respectively. Mycobacterium tuberculosis was isolated in 5.6% and Mycobacterium bovis in 0.9% (only in 1 patient) of cultures. Conclusion: Staphylococcus sp., Staphylococcus aureus, and Aspergillus sp. were the most frequent agents in this cohort. M. tuberculosis should be considered in endemic areas. Detection of infectious agents drives to find adequate treatment and benefits the evolution of patients with CGD.