We present a 35-year-old Japanese man with Crohn disease. He underwent ileocolectomy for ileum perforation when he was 28 years old, Crohn ileitis was diagnosed and medical treatment was commenced. When he was 35 years old, he complained of severe pain of the right upper torso and the left leg with no apparent trigger. A full check-up revealed that he had multiple fractures including a transcervical fracture of the left femur, ribs on both sides, and fracture of the sacroiliac joint. He had no history of prior use of steroids, and the fractures were thought to have been caused by vitamin D deficiency. This case suggests that clinicians should be aware of the possibility of osteomalacia caused by malabsorption of fat-soluble vitamin D when examining patients with ileocolic Crohn disease.