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In this paper, the EU-27 member states banking sector AM251 was analyzed. In doing so, we proposed a shift from the perspective of individual indicators to a comprehensive analysis of a set of indicators. The novelty and contribution is in methodological improvements for early warning and understanding of process of the EU-27 member states banking sector integration using system of indicators. The applied methodology is original to study topology of the EU-27 member states banking sector integration. Additionally, we proposed a simultaneous build up of two comparable models, analyzing the same time period based on a different level of data aggregation. While the former is macroeconomic and draws on aggregated banking sector data for national banking sectors, the latter was compiled from microeconomic data from a pool of banks’ performance data and other micro bank level indicators. The conventional concepts for study of banking sector integration are upgraded with modeling of banking sector integration: macro and micro topologies are developed as integral measure of similarity of the EU-27 member states at macro level and banks at micro level.