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Accepted for/Published in: JMIR Medical Informatics

Date Submitted: Jul 15, 2025
Open Peer Review Period: Jul 16, 2025 - Sep 10, 2025
Date Accepted: Sep 10, 2026
(closed for review but you can still tweet)

The final, peer-reviewed published version of this preprint can be found here:

Implementation of a National Synthetic Data Infrastructure for Privacy-Preserving Analytical Workflows in the Czech National Health Information System: Development and Evaluation Study

Komenda M, Klimeš D, Tichopad A, Jarkovský J, Májek O, Mužík J, Táborský M, Těšitelová V, Habětínek J, Dušek L

Implementation of a National Synthetic Data Infrastructure for Privacy-Preserving Analytical Workflows in the Czech National Health Information System: Development and Evaluation Study

JMIR Med Inform 2026;14:e80683

DOI: 10.2196/80683

Warning: This is an author submission that is not peer-reviewed or edited. Preprints - unless they show as "accepted" - should not be relied on to guide clinical practice or health-related behavior and should not be reported in news media as established information.

Synthetic health data as a catalyst for privacy-compliant innovation: Insights from the Czech National Health Information System

  • Martin Komenda; 
  • Daniel Klimeš; 
  • Ales Tichopad; 
  • Jiří Jarkovský; 
  • Ondřej Májek; 
  • Jan Mužík; 
  • Miloš Táborský; 
  • Vladimíra Těšitelová; 
  • Jan Habětínek; 
  • Ladislav Dušek

ABSTRACT

Synthetic data represent an approach that may potentially address the longstanding tension between the growing demand for primary health data and the imperative to protect individual privacy. By creating synthetic data sets that mirror the structure of real data but do not disclose personal identifiers, the system enables meaningful secondary use for research, policy analysis and innovation. We present the Czech Republic’s synthetic data infrastructure, developed within the National Health Information System (NHIS), as one of Europe's pioneering models for sharing and analysing primary health data. The synthetic data pool is currently being built on the basis of four large national health registries (health services reimbursements, cancer, reproductive health and mortality), with the potential to be expanded to all 61 NHIS agendas. The main principles are transparency and fairness. We describe the process by which researchers and institutions gain access to the synthetic database and develop scripts that are later used to obtain outputs from real patient-level data. We provide examples of such outputs across medical disciplines and aspects of healthcare. The system has already proven its value in the development of national strategies and has been validated by academic, governmental and commercial stakeholders. By adhering to the principles of the European Health Data Space, this model is becoming transferable to other EU countries.


 Citation

Please cite as:

Komenda M, Klimeš D, Tichopad A, Jarkovský J, Májek O, Mužík J, Táborský M, Těšitelová V, Habětínek J, Dušek L

Implementation of a National Synthetic Data Infrastructure for Privacy-Preserving Analytical Workflows in the Czech National Health Information System: Development and Evaluation Study

JMIR Med Inform 2026;14:e80683

DOI: 10.2196/80683

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