The article features an approach to comparative assessments of logistics centres operational efficiency based on the system of logistics key performance indicators and describes the framework methodology and the order for the development of the methodological support of the specified task. The study was conducted in the framework of the Rail Baltica Growth Corridor (RBGC) Russia project, which seeks to involve North-West Russia in the dialogue about Rail Baltica transport corridor and is supported by the Delegation of the European Union to Russia for the period 2012-2013. Particularly, RBGC Russia addresses the issues of operational and functional interoperability of logistics centres in Eastern Baltic Sea Region.