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The harm-benefit analysis (HBA) is a cornerstone of the European Directive 2010/63/EU (the Directive). The Directive regulates the care and handling of animals used for scientific purposes in the European Union (EU). Since its implementation, there has been ongoing debate around the practical applicability of the HBA for research project review processes. The objectives of this study are to analyze the operationalization of HBA in EU member states and investigate the consistency of HBA’s implementation in terms of national legislation and available policy documents. To meet these objectives, we evaluated the transposition of the HBA requirement into national legislation. We also conducted a comprehensive comparative cross-national analysis of all guidance documents pertinent to HBA. The results of our study show that there are (1) deficits in the transposition of the HBA requirement into national laws, (2) significant discrepancies in available policy documents relating to HBA, and (3) insufficiently consistent implementations of HBA in European countries.