Crohn disease (CD) is rare, but the incidence of CD has been increasing over the past ten years. We found two cases of CD, associated with myelodysplastic syndrome (MDS), for the first time in children. In the first patient, MDS was diagnosed at three years of age and CD developed later at eight years of age. The patient presented with recurrent abdominal pain, diarrhea, bloody stools and failure to thrive. Colonoscopy revealed cobble stone like mucosa and mass like lesions with superficial ulceration and inflammatory exudates, observed from the cecum to ascending colon. Ileo-cecal biopsy samples showed ulcers with skipped areas and lymphoid infiltrations. The patient was started on treatment with mesalazine and deflazacort, and symptoms remitted. In the second patient, MDS was diagnosed at nine years of age and CD developed at 13 years of age. This patient has recurrent hematochezia, abdominal pain, vomiting and fever. Colonoscopy revealed a large, deep indurative ulceration on the cecal side of the ileo-cecal valve. Ileocecectomy was done, and histology revealed ulceration with transmural inflammation and lymphoid aggregates. Symptoms improved after ileocecectomy.