Objective To investigate the effect of cultured hair follicle neural stem cells （HFNSCs） on dedifferentiation of macroglial cells in injured optic nerve of rats. Methods Follicle bulge cells isolated from vibrissa pad of male SD rats weighing about 90g were cultured in DMEM/F12 without serum or containing 15% FBS, identified as HFNSCs by immunofluorescence cytochemistry and PCR. The cells were stably transfected with rAAV2EGFP. Adult male SD rats were randomly divided into 3 groups as normal control group, injury group and transplantation group in which HFNSCs were transplanted into injured optic nerves. At 7 days, 14 days and 30 days after EGFPHFNSCs transplantation, optic nerves were observed under fluorescence microscope. At 7 days post operation, optic nerves from injury group and transplantation group were detected by gene chip of Affymetrix and realtime PCR. At 7 days, 14 days post operation, optic nerves were harvested and detected by HE staining and immunohistochemistry. Results Bulge cell in primary culture were labeled by neural progenitor cell markers, however the cells induced by 15% FBS expressed some makers of mature neural cells. EGFPHFNSCs could survive and migrate in the injured optic nerve 30 days after transplantation. With the injury group, there were 240 differentially expressed genes including genes related stem cell, apoptosis, proliferation, transcription, differentiation and development, cell adhesion, signal transduction and so on in the transplantation group. The result of real time PCR was consistent with that of gene chip. There were more cells, more immunoreactivity of Nestin, MBP, Erk1/2, and less immunoreactivity of GFAP in the distal optic nerves and more immunoreactivity of NF in the proximal optic nerves in the transplantation group than that in the injured group. Conclusion HFNSCs regulate some genes expression of glial cells in the injured optic nerve to