Innovation studies are at the forefront of contemporary applied research with public authorities funding annual evaluation of regional and national innovation performance. Numerous innovation indexes are introduced providing the track of innovation trajectories within multiple dimensions. The current study focuses on the multi-level assessment of territorial innovation system capacity. The research methodology is designed to enable the comparison of national and regional level innovation systems. The evaluation procedure is held across 15 individual indicators structured in five dimensions: Human resources, infrastructure, research, innovative milieu, framework conditions. The indicators selected are available for international comparisons in the context of country-region assessment. The research scope is the Baltic region – one of the most innovative macro-region in the world. The study results confirm the strong polarization of the Baltic region in terms of innovation potential and its development dynamics. Lithuania – one of the least performing national innovation systems in 2012, has considerably improved its potential by 2017. The innovation capacity of the North-Western Federal District of the Russian Federation is a third higher than the national average, making it the growth pole of the national innovation system. Top-performing territorial innovation systems are characterized by a strong convergence of all dimensions analyzed. The policy recommendations drawn from the study argue for the coherent development of all aspects of innovation development, ensuring their synergy and cross-fertilization. © 2019, Bucharest University of Economic Studies Publishing House. All rights reserved.