Are messenger bags that bad for your body?

I’m trying to find a bag to use as my everyday carry in college. I thought I’d found the perfect bag (a messenger), until I tried it out on a grocery run. My shoulder didn’t like it, but I didn’t think much of it (it was groceries, after all). However, that did convince me (as did anecdotal evidence on the Net) to try and find a suitable backpack alternative, to literally no avail. If I go back to a messenger, will it screw my body up in the long run?