Conditions That Are Hard to Diagnose Irritable Bowel Syndrome. 1/14. This condition causes pain in your belly area and changes in bathroom habits that last at least 3 months. ... Celiac Disease. 2/14. ... Appendicitis. 3/14. ... Hyperthyroidism. 4/14. ... Hypothyroidism. 5/14. ... Sleep Apnea. 6/14. ... Lyme Disease. 7/14. ... Fibromyalgia. 8/14. More items... Sep 16, 2021