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The potential for multi-criteria decision analysis (MCDA) to support health technology assessment (HTA) has been much discussed, and various HTA agencies are piloting or applying MCDA. Alongside these developments, good practice guidelines for the application of MCDA in health care have been developed. An assessment of current applications of MCDA to HTA in light of good practice guidelines reveals, however, that many have methodologic flaws that undermine their usefulness. Three challenges are considered: the use of additive models, a lack of connection between criteria scales and weights, and the use of MCDA in economic evaluation. More attention needs to be paid to MCDA good practice by researchers, journal editors, and decision makers and further methodologic developments are required if MCDA is to achieve its potential to support HTA.