Objectives. Regulation (EU) 2021/2282 introduces the Joint Clinical Assessment (JCA), a common descriptive clinical evaluation that Member States must take into account in national appraisal. Because national health technology assessment (HTA) systems have developed distinct methodologies, their alignment with the JCA is uncertain. We characterised it across six European jurisdictions and interpreted how the pattern arose. Methods. Qualitative comparative study combining structured expert-consensus rating with documentary process tracing. Two EU-HTA methodologists derived 35 methodological dimensions in five domains from the Regulation, its Implementing Regulation and HTA Coordination Group guidance, fixing and source-tracing the JCA reference position for each before any national rating. Expert pairs in six jurisdictions (France, Germany, Italy, Spain, the Netherlands and England) rated their system against every reference position by consensus, on an anchored three-point qualitative alignment scale. Reporting follows the SRQR. Results. Germany was aligned on 33 of 35 dimensions, with no substantial divergence. England was most distant (23 substantially divergent), followed by France (18); Italy and the Netherlands were intermediate (14 each). Spain recorded no aligned dimension but the fewest substantial divergences of any non-German system (7), diverging in degree rather than in kind. Divergence concentrated in the domains the JCA excludes and in appraisal posture, yet German proximity persisted once these were removed (27 of 29; 19 of 20). Documentary evidence on the legislative compromise, EUnetHTA21 methodological production and subgroup leadership suggests the JCA has emerged as a German-compatible default rather than a neutral synthesis of national traditions. Conclusions. National methodologies align with the JCA to markedly different degrees, the closest fit being the most codified national model. The alignment finding is empirical, the influence account interpretive; neither ranks any national model as superior. Because divergence concentrates where national appraisal remains sovereign, the framework may displace methodological heterogeneity downstream rather than resolve it.

The EU Health Technology Assessment Regulation makes the joint clinical assessment dossier the foundation of a single European appraisal of the relative effectiveness and safety of new medicines, and Article 9 conditions that foundation on the completeness of the evidence a developer submits. Drawing only on the first publicly observable outputs of the new system — two completeness reviews and one completed assessment — this article asks how the European Commission and the HTA Coordination Group are giving operational meaning to “completeness”. It argues that an exacting interpretation is emerging, closer to the logic of systematic review than of regulatory submission, but that the evidentiary base remains too thin to call it a settled doctrine. Two structural tensions follow: a certainty paradox, in which uncertainty is catalogued exhaustively yet never converted into a graded judgment of certainty; and an evidence-generation paradox, in which developers of orphan and highly innovative therapies may face analytical demands whose outcome is largely foreseeable. The article situates these tensions within the principle of proportionality, the duty to give reasons and the limits of judicial review, and sets out a research agenda for the Regulation’s scheduled 2028 evaluation.