Abstract: As more attention is given to people's life and health,China continues to increase investment in scientific research to improve the level of medical research. However,the efficiency of the investment is unknown.In this study,we used the method of data envelopment analysis (DEA) to investigate the input-output relative efficiency of the projects funded by National Natural Science Foundation of China and completed in 2009 at 17 research institutes.We found 11 institutes to be DEA efficient,and 6 to be inefficient.It also showed that adjustment of research structure and setting performance objectives may improve the level of research management and increase the efficency of the investment.