In this paper, quantitative and systematic procedures for establishing Key Performance Indicators (KPI’s) of R&D departments are presented. The proposed methodology is composed of 4 steps : 1) identification of critical success factors, 2) identification of potential KPI’s, 3) determination of KPI’s and 4) monitoring and execution. A Strategy Map has been presented to better align KPI’s with a company’s competitive strategies. Also, Analytical Hierarchy Planning (AHP) is used to determine weights of KPI’s and Data Envelopment Analysis (DEA) is used to analyze the effectiveness of R&D departments. To demonstrate its validity of the proposed method, it has been applied to the R&D divisions of a semiconductor company.