This paper measures and compares the efficiency of national health technology R&D programs focused on translational research program increasing importance using data envelopment analysis (DEA). Three input variables and three output variables are selected for DEA. Inputs are funds, researchers, and project period and outputs are SCI (E) papers, applied and granted patents, and impact factor. This study uses a three-stage approach. In the first stage, output-based DEA model is applied to evaluate the efficiency of decision making unit (DMU). In the second stage, based on efficiency scores of target diseases high-efficiency group and low-efficiency group are classified. And then strategic portfolio matrix of translational research program is composed of four dimensions combining research types. Mann-Whitney U test is then run to compare average efficiency scores among four groups. In the final stage, Tobit regression model is used to estimate factors likely to influence the efficiency. The results are expected to provide policy implications for effectively establishing investment strategy and managing performance of R&D program.