Chronic granulomatous disease (CGD) is caused by mutations in genes encoding nicotinamide dinucleotide phosphate (NADPH) oxidase subunits. A boy was diagnosed as having juvenile sarcoidosis because he presented with cervical and pulmonary lymphadenopathy with epitheloid cells and granuloma formation and high angiotensin converting enzyme. Later, a liver abscess was diagnosed. CGD was established by a dihydrorhodamine 123 (DHR) assay and genetic analysis revealed an unusual intra-exonic splice mutation in the CYBB gene encoding gp91-phox. It did not change the amino acid sequence and allowed for residual NADPH oxidase activity explaining the late onset of the disease. CGD is an important differential diagnosis of juvenile sarcoidosis.