Are Atheist Brains Different from Religious Brains?

Yes they are. According to Grafman's  MRI study of the brain, reported in the PLOS, there are differences between the brain of an atheist and those that believe in God. "People who reported an intimate experience of God, engaged in religious behavior or feared God, tended to have larger-than-average brain regions devoted to empathy, symbolic communication and emotional regulation. "

Above Image:  MRI scan of brain courtesy of jeffrey dach md.

References:

http://www.wired.com/wiredscience/tag/cognition/

In a study published Monday in Public Library of Science ONE, Grafman’s team used an MRI to measure the brains areas in 40 people of varying degrees of religious belief.  People who reported an intimate experience of God, engaged in religious behavior or feared God, tended to have larger-than-average brain regions devoted to empathy, symbolic communication and emotional regulation.  That research, published in March in the Proceedings of the National Academy of Science, suggested that the capacity for religious thought may have bootstrapped a primitive human brain into its current, socially sophisticated form.

The first factor, intimacy with god, was greater in people who had more neurones in an area of the brain that deals with interpersonal relationships.  Now, that's interesting stuff because it shows that people who have a prediliction for feeling intimate with God (praying to god, going to church) may essentially be highly social. 

 http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0007180

Kapogiannis D, Barbey AK, Su M, Krueger F, Grafman J (2009) Neuroanatomical Variability of Religiosity. PLoS ONE 4(9): e7180. doi:10.1371/journal.pone.0007180

Jeffrey Dach MD