We report a patient with longstanding Crohn's disease (CD) developing recurrent sepsis and impaired neutrophil function tests. His inflammatory bowel disease was controlled with local steroids and sulfasalazine with only short exposure to azathioprine. His blood counts remained within normal range, but the marrow showed mild dysplasia. Repeated cytogenetic examinations revealed trisomies 8 and 9, which are typical for therapy related myelodysplasia. Fluorescent in situ hybridization (FISH) study showed stable persistent trisomies, confined to the myeloid lineage, one year after discontinuation of sulfasalazine. The long-term use of immunodulating agents in patients with CD is not without risks, and early therapy related myelodysplasia might not be easily detected by blood count and morphology assessment alone.