MicroRNAs (miRNAs) are noncoding RNA molecules of 21-24 nt that regulate the expression of target genes in a post-transcriptional manner. Evidence indicates that miRNAs play essential roles in embryogenesis, cell differentiation and pathogenesis of human diseases. This study describes a comparison between the miRNA profile of the systemic lupus erythematosus (SLE) patients and the controls to develop further understanding of the pathogenesis of SLE. Peripheral blood mononuclear cells were isolated from blood samples of 23 SLE patients, 10 idiopathic thrombocytopenic purpura patients and 10 healthy controls. The miRNA microarray chip analysis identified 16 miRNAs differentially expressed in SLE. The chip results were confirmed by northern blot analysis. This work indicates that miRNAs are potential diagnosis biomarkers and probable factors involved in the pathogenesis of SLE.