Crohn’s disease is a chronic inflammatory bowel disease, involving gastrointestinal tract and extra-intestinal organs. IgA nephropathy is a rare extra-intestinal manifestation of Crohn’s disease. We describe a case of 21-year old Korean man who was diagnosed with Crohn’s disease 5 years after IgA nephropathy was suspected. At the age of 16, he had gross hematuria and 2 years after he was diagnosed with IgA nephropathy. Three years later, he complained of abdominal pain and diarrhea. He was diagnosed with Crohn’s disease by colonoscopy and histologic exams. There has been increasing evidences of common pathophysiology between the two diseases.