Healthcare decision making is usually characterized by a low degree of transparency. The demand for transparent decision processes can be fulfilled only when assessment, appraisal and decisions about health technologies are performed under a systematic construct of benefit assessment. The benefit of an intervention is often multidimensional and, thus, must be represented by several decision criteria. Complex decision problems require an assessment and appraisal of various criteria; therefore, a decision process that systematically identifies the best available alternative and enables an optimal and transparent decision is needed. For that reason, decision criteria must be weighted and goal achievement must be scored for all alternatives. Methods of multi-criteria decision analysis (MCDA) are available to analyse and appraise multiple clinical endpoints and structure complex decision problems in healthcare decision making. By means of MCDA, value judgments, priorities and preferences of patients, insurees and experts can be integrated systematically and transparently into the decision-making process. This article describes the MCDA framework and identifies potential areas where MCDA can be of use (e.g. approval, guidelines and reimbursement/pricing of health technologies). A literature search was performed to identify current research in healthcare. The results showed that healthcare decision making is addressing the problem of multiple decision criteria and is focusing on the future development and use of techniques to weight and score different decision criteria. This article emphasizes the use and future benefit of MCDA.