Navigating EHDS: Key compliance steps

This European directive is not just another compliance checkbox. Instead, it’s a structural shift in how healthcare data is governed, exchanged, and reused across the EU. For providers, payers, digital health companies, and researchers, this means moving from siloed systems to interoperable, patient-centric, and purpose-bound data flows. The good news: the regulation gives us a clear direction. The challenge: implementing it requires deliberate, incremental planning across architecture, processes, and product.

Your practical checklist

In this article we outline a practical checklist for navigating the EHDS landscape. It is meant to make that path tangible—what to prioritize, what to align now, and how to build foundations that will last.

Scope first: primary vs. secondary use

Inventory your data flows and label them as primary use (care delivery) or secondary use (research, policy, innovation). Obligations differ by category, and the EHDS text explicitly structures requirements around this split ^[1].

Make interoperability a baseline, not a project

Align models and APIs to the European electronic health record exchange format (EEHRxF), which the Commission will specify and update. Expect profiles grounded in FHIR resources, coded terminologies, and machine-readable datasets that EHRs must be able to ingest and emit ^[1][3][4].

Operationalize patient rights

Individuals must be able to access, download, transmit and (where applicable) restrict access to their data via a national “electronic health data access service” (portal/app), including proxy access and rectification flows ^[1][6]. Build these as product features, backed by human-readable audit logs.

Prepare for cross-border rails

Two EU infrastructures matter: MyHealth@EU for primary-use exchange (ePrescriptions, Patient Summaries) and the emerging HealthData@EU ecosystem for secondary-use discovery and access. Design now for conformance and cataloging ^[5][7].

Build for permits, not “data dumps”

Member States will operate Health Data Access Bodies (HDABs)) that evaluate requests and issue data permits. Your pipelines must produce minimally necessary datasets, apply de-identification, and provide provenance inside secure processing environments ^[1].

Security and governance by design

Anchor controls in ISO/IEC 27001 and align with NIS2 where applicable (e.g., incident reporting, supplier risk). Implement zero-trust access, granular RBAC/ABAC linked to roles and purposes, end-to-end encryption & key management, and immutable/queryable audit trails ^[8].

Align analytics & AI early

Maintain model registries, lineage, evaluation reports, and risk logs for anything touching health data. For secondary use, ensure reproducible workspaces (signed notebooks, pinned datasets) that are explicitly tied to a permit and purpose ^[1].

Document once, reuse often

Centralize policies and SOPs (data subject rights, de-identification, incident response, EHRxF/FHIR conformance, DPIAs) in a versioned, living repository your auditors—and teams—can actually use.

EHDS rewards teams that turn compliance into product craft—clean interfaces, predictable pipelines, and verifiable logs.

The EHDS will take time to fully roll out, but the organizations that start aligning today will move faster, face fewer downstream costs, and be better positioned to participate in cross-border care and research ecosystems. Think of this not as a regulatory burden, but as a modernization roadmap: interoperable data as infrastructure, patient agency as a feature, and governed access as a competitive advantage. Start small, document what you do, and build momentum. The goal isn’t perfection—it’s readiness.