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The purpose of this paper is to seek out the problems influencing on the operation of Institution Evaluation(IE) in Korea and suggest a better way for the evaluation based on the findings, expecially focusing on Government Research Institute(GRIs) in the field of Science and Technology. Unlike previous studies on IE of GRIs, this research is more oriented toward actual practices than design and theories of IE. Three categories are 1) purely system aspect, 2) system-operation aspect, and 3) environmental aspect. These three categories are classified into eight sub­categories: 1) the legal support and the legally enforceable provision, 2) the target area of evaluation, 3) the means and process of evaluation, 4) the criteria and indices for evaluation, 5) the expertise of evaluators, 6) the use of evaluation findings, 7) GRIs' support for IE, and 8) public support for IE. Summing up the findings of this study, the main factors that hamper the successful operation of the existing IE of GRIs in the field of Science and Technology was illuminated and the better way for the operation of IE was suggested.