Chronic granulomatous disease (CGD) is a rare disease which has a defect in the generation of microbicidal oxygen metabolites because of defects in any of NADPH oxidase components. As a result CGD patients suffer from recurrent bacterial or fungal infections. A 13-year-old boy was diagnosed with CGD when he was 11 months old. Thereafter he has taken prophylactic antibiotics. In the latest school medical check-up, the chest x-ray showed multifocal patchy consolidation on both upper and lower left lung with small cavity nodule at left upper lung but he did not have any respiratory symptoms. Further evaluations were needed in consideration of his underlying disease. In the chest CT, there was multifocal speculated ground glass opacity and consolidation with or without internal cavity in both lungs. The results of acid fast bacilli stain, tuberculosis culture and tuberculosis PCR-Hybridization of sputum were all negative and interferon-gamma release assay was negative. Galactomannan antigen test for the diagnosis of invasive aspergillosis and fungal culture were also negative. But in the lung biopsy, chronic non-caseous granulomatous inflammation with some fungal hyphae, morphologically favor aspergillosis was identified and Grocott Methenamine Silver (GMS) stain showed some fungal organism. Therefore he has taken the antifungal agent (voriconazole) up to date. This case shows that biopsy is needed independently of the other test results to differentiate the fungal disease.