Neural sciences have recently made great strides in understanding the cellular and biochemical bases of the human behaviors, feelings, attitudes, and beliefs. Since the religious beliefs are among the complicated mental functions that human beings have, and are the products of the brain, they are normally expected to have their reflections in the brain, at anatomical, physiological, and/or biochemical levels. The issue about which cognitive processes or schemas play role on the basis of religions in human beings has intensively being investigated in recent years. There are some cognitive hypotheses proposing that religious beliefs have been developed in order to cope with the fear of death, or they exist because the human brain has been programmed to develop them. It seems that certain brain areas are more important than others in the development of the religious beliefs throughout the evolutional history of the human beings, as well as in individual spirituality. Investigation of the alterations in beliefs emerging in the patients who had lesions on certain brain structures and the observation of the changes in the regional brain activities during religious acts or mystic experiences have presented some new and interesting findings on this topic. Based on these findings, one may conclude that alterations in the functions of prefrontal cortex and temporal lobes particularly, and in the neurotransmitter systems such as serotonin system have crucial importance in the development of the religious beliefs and in the mystic experiences.