European food safety legislation allows for a new type of meat inspection in swine. This ‘risk-based meat inspection without incision’ or ‘supply chain meat inspection’ (SCMI) uses food chain information to derive a veterinary prognosis on the pigs’ health prior to delivery to the slaughterhouse and allows for visual inspection of pig carcasses. Slaughter companies who want to implement SCMI must develop their risk-based system and have it approved by the competent authority. In the Dutch-German border region, slaughter companies implementing SCMI and suppliers delivering pigs in such a system have to consider the prerequisites of a number of competent authorities. In turn competent authorities have to cope with the special conditions and requirements of a cross border economic region. Within the INTERREG-IV-A project SAFEGUARD issues were addressed that arise from the conduct of SCMI in a cross border context. The main objective was to elaborate an up-to-date comparison between Germany and the Netherlands. We used an iterative approach of collecting information from project partners, external experts and scientific literature and providing feedback to the project group during a number of meetings and workshops. We discovered, among others, important differences in ‘involvement of private parties’, ‘data exchange and communication’ and ‘use of epidemiological data’. We conclude that the existence of SCMI systems using different ‘epidemiological data’ from the holding is a barrier to inter-company acceptance of finishing pigs for slaughter. Further, current systems of data exchange fail to give a complete picture of a farm’s health if farms switch deliveries between slaughterhouses. We suggest, that data exchange of food chain information and meat inspection results should be reorganized and harmonized. Further research is needed to assess economic consequences of these issues.