A 13-year-old girl presented with abdominal pain, fever, dysuria, incontinence and pyuria and was subsequently diagnosed as having systemic lupus erythematosus (SLE) with extensive gastrointestinal involvement and an associated interstitial cystitis. Despite aggressive therapy with high dose prednisone and cyclophosphamide she developed a small bowel perforation and subsequently died. The combination of bowel symptoms and interstitial cystitis seems unique to the population with SLE, while the separate complication of bowel perforation carries an extremely poor prognosis in this group of patients.