OBJECTIVES: The aim of this study was to explore how different criteria in HTA influence the final outcome in different drug categories. Next objective was to measure differences in preferences among major stakeholder groups in the Czech Republic. METHODS: RESULTS: The study was completed by 27 (first round) and 13 participants (second round; still ongoing). Clinical effectiveness and quality of life (QoL) were the most important criteria in all groups (relative weight > 11.5%). Policy-makers gave markedly higher weight to cost-effectiveness (CE) and budget-impact (BI). Weights of following criteria were similar in all stakeholder groups: length of life, QoL, unmet need and safety (p>0.31), but for weights of other six criteria there were differences (p<0.03). In multi-criteria assessment, orphan drug showed the highest value of model treatments, but when using the limited set of criteria (only CE and BI) it showed the opposite – the lowest value out of studied model treatments. CONCLUSIONS: Multiple-criteria assessment can add a value to HTA in cases where standard cost-effectiveness analysis is not possible to apply or cannot appraise an entire value (e.g. in orphan drugs). Some categories of drugs can be fundamentally affected by non-complexity of criteria used for the assessment. Overall higher societal value of these drugs may not be fully appreciated via standard Czech reimbursement process. Preferences varied markedly among stakeholders and therefore all should be ideally taken into account.