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I'm currently building up my marathon training again after some time of low mileage running. Unfortunately, I have since developed a bunion, and I've had some pain under the ball of my foot that I suspect is sesamoiditis. I had problems with that before, and some extra padding in my orthotics did the trick Eventually, as I build up mileage, my foot healed and adapated, so I expect that will happen again, but I'm going to the podiatrist to make sure I have the right kind of padding.
The sesamoid bones are small bones in the ball of the foot, below the big toe. If you have been increasing your mileage, or doing speed work or hill work, and you have pain here, sesamoiditis could be the cause. There won't be any visible redness or bruising, usually, and ice can help, but it's important to address whatever biomechanics are involved, so don't hesitate to see a podiatrist to make sure you get it right.