When you have Crohn's disease, your body's immune system begins attacking healthy cells in your GI tract, causing inflammation. Because it is a disease of the immune system, Crohn's is classified medically as an autoimmune disorder.This means that your body is producing antibodies that work against itself.n addition to Crohn's, other autoimmune disorders include rheumatoid arthritis, ulcerative colitis, psoriasis, psoriatic arthritis, ankylosing spondylitis, lupus, and Graves' disease. Inflammatory bowel disease, or IBD, is a category of bowel disorders that includes both ulcerative colitis and Crohn's disease.