Comparative research is a traditional analysis tool in the social sciences. Cross-border cooperation, even within one subregion, namely the Baltics, is characterized not only by general trends, but also by national peculiarities. National specific of cross-border cooperation between Lithuania and Russia and between Estonia and Russia is the object of research of the article. In authors' opinion, cross-border cooperation remains an important instrument of international cooperation of the countries, despite some difficulties. At the same time, cooperation with Lithuania and Estonia matches the common patterns.