The aim of this paper is to emphasise the importance of the institutional support in the process of application and registration of Macedonian agro-food products for PDO/PGI protection. The research was supported with the results of pilot project that study eleven potential agro-food products proposed as eligible for PDO/PGI protection in Macedonia. The field research included a survey of 46 entities and was conducted as a technical support of the Macedonian Ministry of Agriculture, Forestry and Water Economy. The Ministry was at the same time adopting by-laws and rulebooks for establishment of a well defined PDO/PGI protection system. In this respect, we consider this system of protection as a tool for improving the competitive position of the producers, by understanding the current situation in agricultural sector, the problems and constrains and the institutional inefficiencies that appear in the process. The results show that in order to achieve an effective PDO/PGI system, there is a need for strong coordination among the Governmental institutions (Ministry, advisory system, regional offices, etc), the scientific researchers and the producers. This cooperation is crucial in order to provide support in the producers’ decision making process in the registration of products with PDO and PGI protection.