Flow cytometry showed diminished gp91phox expression in the patient's neutrophils suggestive of X-linked CGD.<h4>Conclusion</h4>Our case highlights that early-onset inflammatory bowel disease can be a presenting manifestation of CGD and diagnosis of CGD can be missed if NBT alone is used for screening, especially in the presence of NADPH oxidase activity. The gene discussed is FMO5; the disease is inflammatory bowel disease.