The main objectives of this thesis are as follows : 1) Compare the items that project managers in the public and private R\&D centers consider importantly when they evaluate and select projects. 2) Build a madel that can diagnosis the effectiveness of R\&D project selection system and suggest prescriptions for the better utilization. 3) Compare the effectiveness of project selection system between public and private R\&D centers. 4) Identify the sources of defferences in the perception of project managers and effectiveness of project selection system between public and private R\&D centers and Give some suggestions for the future comparative studies on the performance of research laboratories in the public and private sectors In this thesis, I insist that the generic and structural characteristics which lead to different perceptions of project managers and effectiveness of project selection systems between two sectors are caused by the differences in the ownership, sourece of funding, control mechanism, and the goals and missions imposed on by their constituencies. The model diagnosing effectiveness of R\&D project selection systems consists of three major components. One is the items that project managers consider importantly when they evaluate and select projects, another is the empirically derived project selection criteria, and the other is the determinants of project outcome. I think that the more consitent are the three components, the more effective is a system. Two major hypotheses and ten subhypotheses are tested empirically with data collected from four government-supported and seven private R\&D centers through questionnaire. Wilcoxon Rank Sum test and t-test are employed to test hypotheses. The major findings and implications of this study are as follows : 1) The items that project managers in the public and private R\&D centers consider importantly when they select projects are significantly different. 2) The R\&D project selection system in the public sector is less effective than that in the private sector. 3) These differences are caused by the differences in the ownership, source of funding, control mechanism, and goals and missios. Theses characteristics are so generic and structural that it is hard to modify of change and they should adapt to them. Thus, comparing the performance of research laboratories in the two sectores, we should employ contextadjusted different evaluation criteria or performance standards.