Objective Using proteomics to explore the phasic expression profiles of proteins in rat during foreign nerve regeneration after somatic-autonomic nerve anastomosis. Methods The artificial somaticautonomic nerve anatomosis were established in rats. Foreign nerves and contralateral somatic nerves were collected at 7,14 and 28 days respectively after operation. Extracts of foreign nerves were analyzed by two-dimensional gel eletrophoresis and the differential proteins were measured by matrix asisisted laser desorption ionization time of flight mass spectrometry. The data obtained from peptide mass fingerprinting (PMF) were used in protein database search and the protein identification. Results Mass spectrometric analysis identified 25 proteins displayed different function, including proteins in myeline sheath, inflammatory factors at acute stage, nerve cell cytoskeletal proteins and lipid metabolism proteins etc. The differential proteins may play a part at the process of Wallerian degeneration,axon regeneration and remyelinization. Conclusion Through proteome study we acquired time sequence protein expressions of regenerated foreign nerve,and successfully identified 25 proteins correlated with the process of foreign nerve regeneration. These results suggest that Schwann cells and macrophage cells may play important roles in the process of the foreign nerve regeneration.