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Recent investigations postulate a participation of the interferon regulatory factor-1 (IRF-1) in the development of myelodysplasia (MDS) and in the pathogenesis of autoimmune manifestations (AIMs) in patients with this disease. The aim of this prospective study was to compare the IRF-1 immunoexpression in MDS patients with or without AIMs and to investigate its prognostic relevance. Fifty consecutive MDS patients entered this prospective study. There was no difference in overall survival between patients with or without autoimmune manifestations. In a multivariate Cox regression "IRF-1 expression in immature myeloid cells", Hb, and the IPSS risk group stratification were independent prognostic parameters. Bootstrap resampling confirmed these data. In a multivariate logistic regression older patients with, higher platelet count and increased IRF-1 expression had a higher risk to develop autoimmune-like phenomena. Thus our study shows that IRF-1 plays an ambiguous role in MDS patients. Whereas high levels of IRF-1 in myeloid cells are a favorable prognostic factor for overall survival, they increase the probability of the manifestation of autoimmune phenomena, with a diminished quality of life.