Most people are not perfectly symmetrical, we have one leg that is slightly shorter than the other. But marathon training will introduce you to your biomechanical flaws.
When I was training for my first marathon and running distances longer than 12 miles for the first time, I developed severe pain in my upper left hip, just below the waist. I could barely walk. I called my podiatrist, who recommended a chiropractor or an orthopedist. I went with the chiropractor, but what you need is someone who can take an x-ray and determine whether you have a leg-length discrepancy. If you have a difference of a quarter inch (4-5 mm) or more, a heel lift in the shorter foot will solve the problem, although you may need to wear the lift of the same height in your everyday shoes as well as your running shoes to avoid re-injury.