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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.
In my experience as a Chiropractic Physician, very few times are people actually born with a significant Leg Length discrepancy. (By significant, I mean 1/4", 1/2" or even 1") Leg lengths radiographically are measured in milimeters (mm)and so when we see a leg length of 1/4 inch or more, 9/10 it's actually a musculoskeletal misalignment causing it. Typically it will be either the neck or low back (pelvis or SI joints)that are subluxated or misaligned. These misalignments can cause the local nerves to fire, causing muscle contraction and leading to the leg drawing up higher. Imagine walking or worse, running with that leg length inequality. Over time, it alters your gate, it takes longer for one leg to hit the ground, this sends shocks up the spine and into the joints, creates muscle imbalance and leads to injury. In my time, I have found that I can correct 98% of all leg length issues by simply aligning the spine and pelvis. Indeed there are a small few who actually, legitimately have true leg length inequality that should be corrected or assisted with lifts. Those typically are a result of trauma or illness causing such conditions. To name a few: Polio, born with a club foot, fractures to the Femur and sometimes tibia. Here's the problem, if it's just spinal or pelvic misalignment, and we go and put a lift under that short foot to make it contact with the ground the same as the other, we haven't changed anything. We allow the pelvis to continue skewed and the muscles continue to work and contract abnormally so we havent actually fixed anything, rather we just put a bandaid on it and really just kept the condition the way it was. My recommendation is to get looked at for spinal and pelvic misalignment and if then determined that correction of those can't fix it, then the lift would be the next step.
Excellent points, thank you! I certainly recommend regular chiropractic visits--that has helped me keep up my marathon training!