Methodological naturalism is a strategy for studying the world, by which scientists choose not to consider supernatural causes - even as a remote possibility. There are two main reasons for pursuing this strategy. First, some scientists believe that there is no supernatural: they begin with the assumption that God does not exist (see atheism) and that there is no life after death (see also Atheism and life after death). Second, some scientists believe it is possible that supernatural causes (such as God and angels) may exist, but they assume that any supernatural action would be arbitrary or haphazard and therefore impossible to study systematically.

This kind of approach is the result of application of the epistemology of either of the empirical philosophies of pragmatism or logical positivism, and (because it is a methodology developed without first establishing the ontological principles of the world) is unfounded.

This is the reason that presuppositionalists do not subscribe to methodological naturalism, relying on the intelligent design Programme instead. Presuppositionalists also contend that methodological naturalism is inherently atheistic, since it would be a meaningless exercise to define the rules of empirical inquiry in an entirely arbitrary manner. Since we define the rules of empirical inquiry in such a way that the ontological systematicness of the world is reflected in the method, the methodological naturalist's claim that methodological naturalism is independent of ontological naturalism is disingenuous.