Foot pronation has not been quantified dynamically in three planes of movement in an in-vivo study. The aims of this study were to determine foot pronation through using Principal Component Analysis (PCA) method and to compare it among barefoot, shod and shod with 6◦ lateral wedge during the stance phase of running. In this method, three-dimension of foot movements were measured and each of these components represents a percentage of foot pronation. These components were derived based on eigen- values and vectors of covariance matrix of primary variables. The first (PC1), second (PC2) and third (PC3) components explained about (82.5%, 79.1%), (14%, 15.8%) and (3.5%, 5.1%) the foot pronation for barefoot and shod conditions, respectively. These components were mutually independent and the components set had the same information as the primary variables. Foot pronation index and eversion angles were calculated and compared among barefoot, shod and shod with wedge insole (6◦ lateral wedge insole) conditions in the four phases of stance. Statistical analysis showed that there was no foot conditions effect for foot eversion in four phases (p = 0.72), while this effect was significant for PC1 (p = 0.001). This finding shows that PC1 index could discriminate footwear effect among each phase of stance. Specifically, pronation was reduced in shoe condition as compared to barefoot condition (p = 0.02) from 5 to 50% of stance phase. It has been suggested that the PCA method provides more accurate criteria for investigating effects of footwear interventions on simultaneous three-dimensional foot motion.