Abstract The cytotoxicity of nanomaterials has become a major concern in the field of nanotechnology. The key challenge is the lack of reliable methods to examine the overall cellular effects of nanomaterials. Here, a new method is developed to assess the cytological effects of nanomaterial basing on miRNA expression profiling. The SOLiD sequencing is used to acquire the miRNAs expression profiling in NIH/3T3 cells after exposure to Fe 2O 3 NPs, CdTe QDs and MW-CNTs, respectively. The systematic analysis of miRNAs expression profiling is established by taking account of all miRNAs into their regulatory networks. By affecting the output of targeted mRNAs, miRNAs widely regulated the KEGG pathways and GO biological processes in nanomaterial treated cells. Therefore, the miRNA expression profiling can well reflect the characteristic of nanomaterials, and the method not only provide more evidences to assess biocompatibility of nanomaterials and but also clues to discover new biological effects of nanomaterials.