OBJECTIVES: It became obvious that all countries consider health technology assessment (HTA) differently due to the structure of individual health systems. The objective of this study was to select and establish a new, proper HTA system in Taiwan National Health Insurance.METHODS: A systematic literature review was undertaken to identify relevant papers of each of short tandem polymorphism analysis, positron emission tomography, photodynamic laser therapy and video-assisted thoracic surgery and then used focus group discussion to select category’s aspect, evaluation criteria and schemes of HTA system. Based on analytic hierarch process (AHP) methods, We make interviews with health officials, health care providers and customers by using the AHP questionnaire. Fuzzy multiple criteria decision making (Fuzzy MCDM) was adopted to proceed the empirical evidence analysis and evaluation on the schemes of HTA systems.RESULTS: A total of 65 participants were included in this survey. Three category’s aspect, twelve evaluation criteria and three schemes of HTA system were generated. For the category’s aspect, the sequence of importance is ‘To meet the expectations of health care providers’, then ‘To satisfy the requirements of customer’ and the last is ‘To accomplish the coverage policy of government’ (0.375, 0.337 and 0.238, respectively). The deviation of balancing weight among these three aspects is little and the importance is very similar. The effective score of HTA systems, which is evaluated and selected by whole interviewers, the sequence from large to small is ‘system of safety and efficacy’, ‘system of ethical standards’, and ‘system of cost effectiveness’ (67.18, 61.41 and 58.01, respectively).CONCLUSIONS: The ‘system of cost effectiveness’ is not suitable to adopt at current stage. It does not meet the expectations from health care stakeholders if there is only one HTA system. The Bureau of National Health Insurance should select ‘system of safety and efficacy’ as the basis to establish a new, proper HTA system in Taiwan.