There could be lots of causes for it, but it could be the same basic back pain that is the #1 leading cause of missed work and doctor's appointments... working out doesn't change the fact that we spend a lot of our time in a seated position.
Exercise related injuries can make it worse, and there is also the problem of overcompensating for injured areas without really realizing it.
I get a chiropractic adjustment once a month, and it has done wonders for my lower back and neck problems; I really believe that misaligned discs can lead to ill health and bad posture, which feeds on itself.
Obviously if you're worried about kidneys or other problems like that you need to get it checked out.
Just don't keep grinding your lower back with heavy squats if you have a chronic injury. Sometimes there is such a thing as too much intensity.