Reduce the use of antimicrobial compounds in livestock production is necessary to limit antimicrobial resistance development and to protect the health of animals, humans and ecosystems. This complex task may only be accomplished via the implementation of a systemic approach, which takes into account the management of animal health as a whole, avoiding simplistic strategies. To that purpose, 15 scientists working on different domestic monogastric species (pig, poultry, rabbit) formed the consortium ‘RIMEL’. We propose an interdisciplinary conceptual framework for the evaluation and management of animal health. This conceptual framework listed 11 fundaments of animal health organized in two main dimensions. The first one, physical health, refers to the association of barriers (skin, mucosae and microbiota) and defenses (innate and acquired immunity, and nervous and endocrine systems). The second one considers the psycho-social health (mother-young interactions or amongst relatives, the expression of the innate behavioral repertoire, and the respect of circadian rhythm). We identified critical periods for health in each species related to the maturation dynamics of each fundament. Then, we associate these fundaments with various indicators of health status (zootechnical performance, behavior, metabolic or hormonal markers, etc.). Finally, the framework takes into account more than 30 practices applied in the long- or in the short-term to drive health in livestock systems (genetics, reproduction strategy and renewal management, feeding, hygiene and prophylaxis, living environment, etc.). We organized all the elements to describe the biological relays, to distinguish levers and risks, and to build a representation that took into account the lag between actions and results on a targeted population. This framework is a tool to (1) help and structure research on integrated management of animal health (2) characterize and analyze existing systems, (3) design and evaluate innovative practices and systems. Our ultimate goal is to support the transition of animal production towards systems with low antimicrobial inputs.