We describe the first reported case of a spontaneous septic arthritis caused by Burkholderia cepacia, the organism responsible for onion skin rot. The source of infection was most likely from hematogenous spread, as the patient's blood cultures were positive for B. cepacia. Treatment involved arthroscopic irrigation and drainage of the affected shoulder. Despite post-operative resolution of this immunocompromised patient's shoulder symptoms, he was unable to survive the B. cepacia bacteremia. Our report not only describes the case but also reviews the difficulty in treating B. cepacia infections.