Objective To investigate changes of gene expression in hippocampal radial glial cells activated by hippocampal extracts EM>in vitro/EM> .Methods Extracts were successfully prepared from normal and deafferented hippocampi after fimbria-fornix transection. Radial glia cells (RGCs) from the hippocampus of newborn rats were divided into two groups: the normal group treated with extracts from normal hippocampi and the transected group treated with deafferented hippocampal extracts. After 7 days of incubation, cells were subjected to immunofluorescence against vimentin and nestin. Total cellular RNA was extracted and transcriptional level was determined using affymetrix microarrays. Quantitative PCR was performed directly towards several genes related with the differentiation of neural stem cells. Results Compared with the normal group, more vimentin and nestin double positive cells were observed in the transected group. Treatment of deafferented hippocampal extracts significantly increased the area and perimeter of double-labeling cells. Affymetrix microarrays detected a total of 709 genes, ten of which increased by 2 folds and ten decreased by 2 folds after treatment with deafferented hippocampal extracts. Quantitative PCR indicated that two neuronal differentiation-related genes increased in micrarrays were up-regulated significantly after cells were treated with deafferented hippocampal extracts.Conclusion Fimbria-fornix transected hippocampal extracts can activate the RGCsEM> in vitro/EM> and the two neuronal differentiating related genes, Rest and Runx1t1, increase in the activated RGCs.