As part of a health technology assessment, economic evaluation of health technologies for rare diseases poses specific challenges given that such technologies are rarely cost-effective. Therefore, conventional economic evaluation techniques appear to be less relevant to health technologies for rare diseases. However, the definition of health technology assessment points to multi-criteria decision analysis by stating that a health technology needs to be assessed against multiple criteria in order to pronounce a judgement about the value of the health technology. Thus, this editorial argues that a full health technology assessment which uses a multi-criteria decision analysis framework to evaluate the value of a technology can be applied to health technologies for rare diseases. Past experiences demonstrate that the specific characteristics of health technologies for rare diseases can fit in the conventional health technology assessment paradigm by means of multi-criteria decision analysis.