Objective To study the effect of pre-degenerated common peroneal nerve on apoptosis and proliferation in injured rat optic nerve. Methods One hundred and fifteen adult male rats were divided into normal, injured and transplantation group. Cell number, apoptosis/proliferation, proliferating cell nuclear antigen(PCNA) expression and apoptosis/proliferation related gene expression in rat optic nerves were examined respectively using HE staining, flow cytometry, Western blotting, gene chips and real-time PCR. Results Cells in the optic nerve of the injury group increased compared with that in the normal group, but was lower than that in the transplantation group. Compared with the normal group, apoptotic cells increased and proliferated cells decreased in the injury group; Compared with the injury group, apoptotic cells decreased and proliferated cells increased in the transplantation group. Compared with the normal group, PCNA expression was downregulated in the injury group, but PCNA expression was up-regulated in the transplantation group than that in the injury group. Compared with normal group, thirty seven apoptosis and proliferation related genes expressed differentially in the injury group; Compared with the injury group, three genes expressed differentially in the transplantation group. Conclusion The cellular apoptosis increases and the cellular proliferation decreases in the distal part of the optic nerve after the optic nerve injury. Autograft transplantation of the common peroneal nerve could reduce the cellular apoptosis and promote the cellular proliferation. In addition, some corresponding gene expressions changed.