In the present article, the author considers a role of religious institutes, which are institutionalized generally in the form of the international non-governmental organizations of a religious orientation in globalization conditions of the modern international relations. The role of the religious organizations in world politics and their place in system of Political Science institutes of the contemporary world are described. Besides, the author reveals and analyzes paradox of replacement of qualities and functions of the non-governmental organizations of a religious orientation determined by their institutional nature, by new, uncharacteristic for them and arisen as a response to tendencies of transformation of non-governmental organizations of a religious orientation from the independent subject of the international relations into the tool of foreign policy of the concrete states.