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This study was designed to analyse the efficiency of regional R&D investment in Korea by employing DEA(Data Envelopment Analysis) Model. The government budget for Science and Technology, National R&D investment for region and numbers of regional R&D researcher are the input-variables of the analysis, whereas the output-variable is GRDP. The result shows that the Technical Efficiency - both of Pure Technical and Scale one - has been declining ever since 2003; this means that regional R&D investment is not proportional to GRDP. We also have tried a comparative analysis among regional R&D investment efficiency with the data of 2008 and the average value during 2003∼2008 as well. Results of the analysis show that in 2008, Seoul, Gwangju, Gangwon, Chungnam,Jeonnam and Jeju are efficient in the first data set, while Seoul, Gwangju, Daejeon,Chungnam, Jeonnam and Jeju are efficient in the second data set. Jeonnam, Seoul and Chungnam are reference (bench-marking) regions based on BCC model in the first data set,and Jeonnam, Seoul and Gwangju are alternatives in the second data set.