This study was purposed to clarify the difference of microRNA (miRNA) expression in the peripheral blood cells of patients with primary immune thrombocytopenia (ITP) and normal controls. Exqion miRCURY(TM) microarray was used to investigate differentially expressed miRNA of peripheral blood cells obtained from affected ITP patients and the healthy controls. Cluster analysis was used to identify miRNA expression profile between the ITP patients and the healthy controls. Real-time PCR was used for validation. The results showed that a total of 159 miRNA were found to be differentially expressed in ITP patients compared to the controls, with 79 up-regulated and 80 down-regulated. Based on these differentially expressed miRNA, a tree with clear distinction between the controls and ITP patients was generated by cluster analysis. Real-time PCR confirmed microarray analysis results. It is concluded that differentially expressed miRNA were found in the peripheral blood cells from ITP patients, which may be potential novel biomarkers for ITP as well as help to elucidate pathogenic mechanisms of ITP.