Chronic granulomatous disease (CGD) is characterized by granulomatous inflammation of multiple organ systems secondary to a defect in the ability to generate reactive oxidative species. The most common and severe form of CGD is an X-linked recessive disorder attributable to a defect in the gene encoding the gp91phox subunit of NAPDH oxidase, which is involved in microbial killing. This defect predisposes individuals to severe and recurrent bacterial and fungal infections. Ocular manifestations include keratitis and chorioretinal lesions. The pathogenesis of the chorioretinal lesions is unknown. We describe the first case, in which Pseudomonas aeruginosa (P. aeruginosa) DNA is detected in the chorioretinal lesion of an 18-year old male with CGD who expired from multiple systemic infections including P. aeruginosa pneumonia following intensive immune suppression for inflammatory bowel disease. Our detection of P. aeruginosa molecular signature in the eye offers insights into the pathogenesis of ocular lesions seen in CGD.