Objective To analysis and compare the proteomic differences between neural stem cells and motor neurons in embryonic spinal cord in rat and discover the key different proteins. Methods Separating the protein of cells by the 2-D fluorescence difference gel electrophoresis, and to analyse the differences of protein expression with DeCyder software, and to identify with high performance liquid chromatography-electrospray tandem mass spectrometry. Results About 1 300 protein spots from the cells were gained after gel analysis. Eighty-seven protein spots were selected for mass spectrometry analysis. Fourty-four differently expressed proteins (24 in neural stem cells and 20 in motor neurons) were identified by mass spectrometry analysis. Conclusion Differently expressed proteins between neural stem cells and motor neurons were identified and it is helpful to find the new targets in neural stem cells differentiation into motor neurons.