This chapter presents Agazzi's considerations on the relationship between science and religion. In the first part I discuss Agazzi's analysis of natural and empirical science, which can be seen as a source of the modern and systematic conflict with religious belief, if science is interpreted according to logical positivism. This interpretation mainly means taking the scientific perspective (i.e. physical objectivity) as closed, precluding any metaphysical view. In the second part I focus on the positive relationship between metaphysical insight and religious faith, which is a necessary condition for the harmony between science and religion. I will especially highlight Agazzi's notion of rational faith as a helpful element in a correct understanding of the problem tackled in this chapter. Faith and reason are necessary interactive elements both in natural science and in philosophy or metaphysics.