A boy developed ipsilateral axillary lymphadenitis after Bacillus Calmette-Guérin (BCG) inoculation at the age of 5 months. Subsequently, he was diagnosed with X-linked chronic granulomatous disease (CGD) by the nitroblue tetrazolium assay when he was 4 years old. Body computerized tomography (CT) performed at the age of 25 years showed enlarged lymph nodes in the left periclavicular and axillary regions, and was confirmed by gallium scintigraphy. Mycobacterial culture, smear, and polymerase chain reaction (PCR) of the sputum and gastric fluid were negative. Whole-blood IFN-gamma assay was negative as well. Mycobacterium bovis BCG was isolated from the lymph node biopsy by PCR amplification and culture. No mutation of the IFN-gamma receptor 1 could be identified. In conclusion, CGD can be the underlying condition for BCG-itis; whole-blood IFN-gamma assay might be useful in differentiating BCG infection and tuberculosis in CGD patients; BCG vaccination is contraindicated in X-linked CGD.