Scientific American has an interesting article summarizing what is known about the neurophysiology of meditation and religious experiences. The article does a good job describing the science, but in the end takes a deliberately agnostic view about the meaning of the results. Here are some excerpts:

Spiritual neuroscience studies also face the profound challenge of language. No two mystics describe their experiences in the same way, and it is difficult to distinguish among the various types of mystical experiences, be they spiritual or traditionally religious. To add to the ambiguity, such feelings could also encompass awe of the universe or of nature. “If you are an atheist and you live a certain kind of experience, you will relate it to the magnificence of the universe. If you are a Christian, you will associate it with God. Who knows?

…Moreover, no matter what neural correlates scientists may find, the results cannot prove or disprove the existence of God. Although atheists might argue that finding spirituality in the brain implies that religion is nothing more than divine delusion, the nuns were thrilled by their brain scans for precisely the opposite reason: they seemed to provide confirmation of God’s interactions with them. After all, finding a cerebral source for spiritual experiences could serve equally well to identify the medium through which God reaches out to humanity. Thus, the nuns’ forays into the tubular brain scanner did not undermine their faith. On the contrary, the science gave them an even greater reason to believe.