This just seemed, by definition, the place to share this. Someone askied in Straight Answers about 9 years ago. Stock answer; Pope Gregory, plague, yatta yatta.
I don’t think that’s it. It may have started then, but I have a theory that the reason has been lost to us in the mists of time. I’d like to think that “God Bless You” was something they said when a sneezer covered up his or her (public) sneeze effectively. And that somewhere along the line, the line just became an empty formula upon hearing a sneeze. The sneezer was actually being blessed for a reason.
I had always heard that in the Dark Ages, people believed that the soul came out of the body for a moment when you sneezed, and old Scratch was just waiting to grab it. Saying Gawblessya prevented that from happening.
I thought this would go “but we don;t say ‘God damn you’ when someone farts.”
Folklorist chiming in, terminology first:
Saying something after a sneeze is a custom.
The idea that we should practice the custom is a (folk) belief, as is any given notion about the origin of the custom.
Sometimes there is a story explaining the origin of the custom, which is a type of legend built around a belief.
Since all three of these are genres of folklore, they all exist in variation. The origin of the custom is not known. There are several different beliefs and legends about the origin of the custom. Some are older than others, so we can rule some out (attaching Pope Gregory’s name to is more recent than the idea that it’s a superstitious response to illness, for example). My reference books are still in storage so I can’t quote sources, but my memory is that the “magically prevent soul from escaping” and “magically prevent sneezer from getting a more serious illness” are top contenders, but without proof. All others are disprovable because they either make no sense, contradict evidence, or are demonstrably more recent beliefs / legends.
ETA: just saw the fart comment. We don’t say the same thing, and we don’t give the same reason, but the custom is basically the same: after an involuntary bodily noise, we say something. “Bless you” and “Excuse me” are two sides of the same coin.
SDStaff songbird wrote a column about this as recently as 2001.