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A well-functioning swine health system is crucial to ensure a sustainable pig production. Yet, little attention has been paid to understand it. The objective of this study was to unravel the complexity of a swine health system by using a system-thinking approach for the case of Flanders (Northern part of Belgium). To that end, qualitative interviews were held with 33 relevant stakeholders. A hybrid thematic analysis was conducted which consisted of two phases. First, an inductive thematic analysis was conducted and secondly, the resulting themes were classified into the building blocks of a systemic framework. This framework combined a structural and a functional analysis that allowed to identify the key actors and their functions. Additionally, a transformational analysis was performed to evaluate how structures and the entire swine health system enable or disable functions. Findings revealed that the Flemish swine health system presents several merits such as the synchronization of policies and sector’s agreements to reduce the antimicrobial use in the pig sector and the presence of a rich network of universities and research institutes that contribute to the education of health professionals. Nevertheless, several systemic failures were observed at different levels such as the lack of a good professional body representing the swine veterinarians, the tradition that veterinary advice is provided for ‘free’ by feed mill companies, and the shortage of reliable farm productivity data. Both latter failures may hinder swine practitioners to provide integrative advice. While few veterinarians are remunerated per hour or per visit by farmers, the most common business model used by veterinarians is largely based on the sale of medicines. Thus, veterinarians encounter often a conflict of interest when advising on preventive vaccinations and in turn, farmers distrust their advice. On a positive note, alternatives to the traditional business model were suggested by both veterinarians and farmers which may indicate that there is intention to change; however the broader institutional and socio-cultural environment does not enable this evolution. The results of this present study can aid policy makers to anticipate the effects of proposed interventions and regulations so that they can be fine-tuned before they are enforced.