The paper is authored by the heads of the research project «The Development of a New Methodology for Dialogue and Cooperation between Science and Religion in Russia» (supported by John Templeton Foundation). The paper gives an overview of research results. The traditional dialogue (within Christian cultural tradition), which was largely epistemological, should be made wider and deeper thanks to new approaches — in particular looking comparatively at the very ethos of the scientific and religious communities. This aspect is most significant in Russia given the character of post- Soviet transition. Science and religion are not just the two different methods of knowledge but also the two different social institutions and cultural traditions. Now the context of their interaction is the crisis of modern paradigm of functional differentiation of society, as religion acquires wider public acclaim while science loses cultural hegemony. In these new circumstances, the dialogue opens some new perspectives: comparison of metaphysical foundations of both science and religion; exploring macro- and micro-social contexts in the production of scientific and religious knowledge; productive meeting of theology with social / human sciences.