Chronic granulomatous disease (CGD) is caused by gene mutations that affect the phagocyte NADPH oxidase. This results in recurrent infections by catalase-positive bacteria or fungi. Here, we report a case of X-linked CGD presenting a mixed infection with Burkholderia cepacia and Aspergillus. A novel mutation was found by bioinformatics analyses of his genealogy (c.1234delG), which perhaps changed the structure and function of the related proteins.