An eight-year-old castrated male Domestic Shorthair cat was presented to the Cornell University Hospital for Animals for a six month history of chronic diarrhea. Multiple treatment modalities did not result in resolution of clinical signs so the patient was referred to Cornell University’s Internal Medicine Service. The only abnormalities on physical examination were a grade II/VI left sided heart murmur and fluid-distended intestines. Bloodwork was within normal limits. An abdominal ultrasound detected moderate, diffuse colopathy. An upper and lower endoscopy revealed blunted and edematous duodenal villi and severely nodular and ulcerated colonic mucosa. Histopathology diagnosed alimentary lymphoma in the small intestine and an inflammatory process of the colon. FISH analysis of colonic tissue revealed evidence of ulceration and deep bacterial invasion of the mucosa. The patient was treated with pradofloxacin while results were pending and then prednisone and chlorambucil were added to his treatment protocol.