Aspergillus nidulans is one of the several species of Aspergillus with low pathogenicity. The significant infections of A. nidulans in human have rarely been reported, almost exclusively in patients with chronic granulomatous disease (CGD). CGD is a primary immunodeficiency disease which results from the absence of the NADPH oxidase in the phagocytic cells, leading to recurrent pyogenic infection and granuloma and abscess formation. Here we report a fatal case A. nidulans infection in a six-year-old boy with chronic granulomatous disease. A. nidulans was isolated from the culture of a paraspinal abscess and Aspergillus was detected in the surgical tissue by in situ hybridization. The patient succumbed despite prolonged treatment with high-dose amphotericin B, itraconazole and interferon-alpha. To our knowledge, this is the first report of A. nidulans infection in Korea.