We examined microsatellite instability (MSI) at 10 loci of dinucleotide repeats using the polymerase chain reaction (PCR) in patients with myelodysplastic syndrome (MDS). Bone marrow DNA was obtained from 45 patients repeatedly during the disease course and fibroblast DNA was also collected from 19 of them as a normal control. Three of the 19 patients showed an alteration at more than three loci, when the allele length was compared between their fibroblast DNA and the initial marrow DNA. On the other hand, none of the 45 patients showed an alteration when the initial sample was compared with the latest one. One of the three patients with MSI had refractory anemia and two refractory anemia with ring sideroblasts and none of them showed disease progression, complex chromosome abnormality, karyotypic evolution, or mutation of N-RAS or TP53. Moreover, a frameshift mutation within 10 repeating adenines of transforming growth factor beta type II receptor gene, which was recently recognized as a critical target of MSI, was not found in any of the patients including the three with MSI. These findings suggest that MSI is an early but infrequent genetic event and is independent of other critical genetic aberrations in the development of MDS.