We describe a 9-year-old girl who presented with abdominal pain, found incidentally to have multiple liver granulomata. Extensive autoimmune and infectious workup was negative. The patient had esophagogastroduodenoscopy and colonoscopy, confirming the diagnosis of Crohn's disease. Hepatic granulomata are a rare complication of Crohn's disease and are often secondary to pharmacotherapy or infection in immunosuppressed patients. This case, to our knowledge, is the first reported case of a pediatric patient diagnosed with Crohn's disease after initially presenting with hepatic granulomata as an extraintestinal manifestation of the disease.