Chronic interstitial cystitis and ureteral stenosis has occasionally been reported in systemic lupus erythematosus, mostly associated with gastrointestinal symptoms. We report a case of obstructive uropathy associated to chronic interstitial cystitis as the only manifestation of lupus flare in a patient with SLE and anti-phospholipid syndrome (APS) who had been in remission for many years. The development of chronic interstitial cystitis in patients with SLE and APS has not been previously reported. Histopathological study of her urinary bladder and ureteral meatus showed chronic inflammatory infiltrate in the subepithelium. Lack of significant lower urinary tract symptoms and gastrointestinal involvement were some of the factors that could have prevented an earlier diagnosis. Obstructive uropathy and renal insufficiency initially improved with immunosuppressive treatment and endoureteral protheses, but poor compliance to the therapy led to ominous ending.