A 28-year-old man developed Crohn's disease and myelodysplastic syndrome concurrently. Chromosomal analysis of the bone marrow revealed a normal male karyotype. Subsequently, the myelodysplastic syndrome progressed to acute myelocytic leukemia. Several causes, including the medical treatment for Crohn's disease, chromosomal abnormalities, and a common underlying immune dysfunction, have been proposed as pathogenetic factors in the association with Crohn's disease of hematologic malignancies. This case suggests that neither medical treatment for Crohn's disease nor chromosomal abnormalities are inevitable causes of the development of hematologic malignancies associated with Crohn's disease. At present, the cause of the association remains unclear, although the idea of a common immune dysfunction is attractive.