A comprehensively designed Pharmaceutical Quality System (PQS) incorporating Good Manufacturing Practice and Quality Risk Management implemented, maintained and continuously improved, allows a consistent delivery of products with appropriate quality attributes. The manufacturer in the third country and the batch certification and release site in EU belong to the same organization operating under a corporate Pharmaceutical Quality System. A signed Quality Agreement between both parties provides improvement of the Pharmaceutical Quality System and continual maintenance of the quality of the medicinal product throughout its shelf life. This paper outlines the role and the challenges of the manufacturing site in third country within the process of batch certification and release in EU (by EU QP) and also highlights the importance of the technically justified approach including Quality Risk Management process regarding sampling in third country. Through a Technical justification for sampling including Quality Risk Assessment, it is considered that the samples taken from the manufacturing site in third country ensure representation of the whole batch. Technical justification is performed periodically to identify and manage any risks associated with this approach, thus ensuring the quality, safety and efficacy according Marketing Authorization. Keywords: batch release in EU, third country, Pharmaceutical Quality System, QP