Recently, the microRNA (miRNA) signature has been used for better characterization and understanding of the pathogenesis of different malignancies, including myelodysplastic syndromes (MDS). MDS are a heterogeneous group of stem cell disorders in which the genetic and molecular defects are not well defined. In the present study, we applied array based miRNA profiling to study 19 bone marrow cell samples of de novo MDS compared with eight healthy individuals. In addition, integration of the miRNA profiling data with our previous array comparative genomic hybridization data, from the same cohort of patients, was performed. We observed up-regulation of hsa-miR-720 and hsa-miR-21, and down-regulation of hsa-miR-671-5p and one human virus miRNA (Epstein-Barr virus miR-BART13) in MDS samples compared with normal samples. In our study, the copy number alteration harboring miRNA was not affecting miRNA expression, but a distinct microRNA expression pattern was observed, not only in MDS compared with controls, but also between MDS entities.