The 3Rs (namely, Replacement, Reduction, and Refinement) and harm-benefit analysis (HBA) are central to the evaluation procedures regulating the use of animals in biomedical research. These deeply intertwined frameworks frequently overlap conceptually and are often confused. This paper examines whether these frameworks are grounded in the same moral factors to descriptively investigate the normative functions attributed to them in recent publications and in Directive 2010/63/EU. To this end, the strategies for operationalising the 3Rs and HBA were examined to infer the ethical issues researchers typically face by identifying and clustering the most recurring themes and arguments mentioned in the literature. This conceptual ‘unpacking’ process concludes that the moral factors underpinning both frameworks centre on two main normative anchorage points: the Animal and Epistemological foci. A set of normative, operational criteria relevant to ethics committees when assessing research project proposals was also developed.