Contemporary neuroscience research aims at elucidating human brain function with regard to its temporal evolution and the underlying brain structures Over the last decade of the 20th century systems physiology has advanced our understanding of sensory perception, control of action, and cognitive processes. More recently, however, the relation of brain function and the humanities has come into focus in brain science. Functional neuroimaging was used to test the hypothesis that the mental processes underlying philosophical and religious reasoning are domains of normal human brain function which therefore are accessible physiologically. Here, it will be shown that religious experience is accomplished by various mental strategies as evident from different experimental approaches and cerebral activation patterns. Nevertheless, the similarities of the reported activation patterns in the medial prefrontal and adjacent paracingulate cortex across the different studies suggest a common role of subjective attribution of intentionality (theory of mind). Further, since religious experience was perceived and could be labeled as such by the subjects, the conceptional existence of this mental process is supported. Conversely, the topography of the related activation patterns in the human brain opens a neurobiological approach for improving the understanding of the underlying mental processes. Based on these preliminary data perspectives for the experimental design of future studies addressing the neuroscientific basis of transcendental reasoning are presented.