Idiopathic thrombocytopenic purpura (ITP) and primary myelodysplastic syndrome (MDS) are hematological disorders that are frequently associated with thrombocytopenia, and both are heterogeneous disorders of uncertain etiology. Their diagnosis requires the exclusion of other hematological or immunological disorders whose diagnosis is usually not difficult. However, in some patients presenting with thrombocytopenia, the differential diagnosis is complex. We performed a retrospective study of 47 consecutive patients treated between 1990 and 2001; in 25 patients the initial diagnosis was ITP, in 22 it was MDS; we compared their backgrounds, laboratory data and clinical outcomes. Among the 25 ITP patients, there were 5 confusing cases. Following treatment, they presented with inexplicable refractory anemia and/or neutropenia. Cytopenia, the polyploidization pattern of megakaryocytes, and chromosomal aberrations were of diagnostic relevance in these patients’ defective hematopoiesis. Their cytopenia progressed relatively slowly and none progressed to leukemic transformation. We suggest that these 5 patients should be classified into an unusual subtype of MDS with clinical characteristics resembling ITP.