The author presents the thesis assumed by most scientists that the principle of methodological naturalism is a necessary condition of science. He also shows the role of this thesis in the context of the relationship between science and religion (by religion he means here Christianity). He tries to show that contemporary science does not leave any gaps in our knowledge that would call for any supernatural or transcendent sphere of being, postulated by religion. Christianity admits events in the history of the universe in such a way that for their explanation it is necessary to appeal to supernatural agents disrupting the order of nature. If this is so, then we can claim, he argues, that contemporary science is incompatible with Christian doctrine. The author also argues that if we assume a realist interpretation of scientific theories, formed on the basis of methodological naturalism, and if we take into consideration the role of science in contemporary culture of the Western civilisation then we should consider the scientific model of realty as making atheism a more rational option.