This research examines performance evaluatees' opinions regarding the institutional performance evaluation systems of Government S&T Research Institutes (GRI). Research methodology is as follows: first, four perspectives of Kaplan & Norton (1992) Balanced Scorecard Model are revised into six perspectives suitable to GRI's characteristics. Second, experts classify current performance evaluation measures into the six perspectives. This enables different evaluation systems of three GRI evaluation groups to be compared under the same evaluation measures. Third, GRI's evaluatees are asked to allocate ideal weights on the performance measures. The evaluatees' weights are compared with the weights of current performance measures, and the characteristics of evaluatees' opinions about current performance evaluation systems are analyzed. Results are as follows; first, six perspectives for Korean GRIs are financial, long-term outcome, short-term outcome, strategic direction, project management, human resources perspectives. second, GRI evaluation systems put the most weights on the long- and short-term outcome perspectives and the least weights on the financial perspective. This result complies with theoretical model: in performance evaluation of GRIs, the customer perspective is the most important one while the financial perspective is the least important one. Third, evaluatees think that the long-term outcome perspective of the Basic-technology GRI group and the short-term outcome perspective of the Applied-technology GRI Group needs more weight. Fourth, it is found that the current systems have more weights on the project management and strategic direction perspectives than evaluatees think. The possible explanation of this result would be that since the measures of these perspectives are relatively easier to set up than those of other perspectives, the current systems contains larger number of measures and, accordingly more weights.