From Tom Rees of Epiphenom:

Sam Harris, author of The End of Faith, has just published a brain imaging study of religious belief. Harris and his colleagues were interested in two questions. Firstly, how does the brain process ideas of “belief” and “disbelief”—and does it differ when you are talking about religious beliefs or other kinds of beliefs. Secondly, which bits of the brain evaluate religious beliefs, and do they differ from the evaluation of nonreligious beliefs.
What they found was that different bits of the brain light up when you evaluate a statement that you believe to be true compared with one that you believe to be false. And it really doesn’t matter whether you are a believer or a nonbeliever, or whether the statement is a religious one or a nonreligious one.
What matters is whether you personally believe it to be true or false.
In other words, a believer will evaluate a religious claim that “The God of the Bible is literally true” in the same way that a nonbeliever will evaluate the statement “The biblical god is a myth.” And they will both evaluate these in the same way as the statement “Santa Claus does not exist.”
But where the study did find a difference was for religious claims in general (whether or not they were believed to be true). That’s what the image at the top of this post shows. It’s the parts of the brain that light up when processing a religious claim compared with a nonreligious claim.
So what does this prove? Well, part of the problem with these kinds of studies is that they don’t show much. The brain is a complex, poorly understood organ, and each bit of the brain has been linked to several different functions.
With that caveat, Harris reckons that the evaluation of religious statements seems to be linked to emotions of disgust and pain. On the other hand, nonreligious statements are linked to regions of the brain connected with memory and semantic evaluation. If that’s the case, then it would seem to support the idea that nonreligious claims are decided by a logical evaluation, whereas religious claims are decided according to whether they disgust you or not.
And a last little tidbit. There was also a difference in how quickly the subjects evaluated the statements. The quickest response times were for the nonbelievers when evaluating religious claims they agreed with (i.e., “The biblical god is a myth”). In general, it’s quicker to evaluate a “true” statement than a “false” one. Could it be that “Religion is false” is more true for nonbelievers than “Religion is true” is for believers?