I was on Topamax forever and I have a family history of Kidney stones, so while taking Topamax I had kidney stones (started with flank pain) several times.
I even had a discussion with my doctors and agreed to keep taking topamax KNOWING that it was contributing to kidney stones. I agreed to do this even if it meant I had kidney stones twice a year since the topamax was working so well for my migraines.
Have you ever had kidney stones? Do you know the symptoms? Regardless, I would talk to the doctor and at least inform them of how you are feeling.