Excessive pronation in running is known to be one of the dominant causes of running injuries. In order to prevent it, the trilateral relationship of pronation, foot anatomy, and shoe structure has been studied in detail up to now. In addition, we assumed that the foot position at the heel contact (HC) and running speed could also affect pronation significantly. Then, we studied the relationship among foot motion, shoe sole stiffness and running speed using a multi-regression analysis. We conducted several experiments using 11 experienced runners, an optical motion capture system, a treadmill with two different speed and two types of running shoes with different inner-sole stiffness. Consequently, in low-stability shoe, pronation could be estimated primarily by foot position at HC and this relationship between them depended upon running speed. In high-stability shoe, on the other hand, the same relationship could not hold, probably due to other primary personal factors.