Objective. To quantify the effects of medial foot orthoses on skeletal movements of the calcaneus and tibia during the stance phase in running. Design. Kinematic effects of medial foot orthoses (anterior, posterior, no support) were tested using skeletal (and shoe) markers at the calcaneus and tibia. Background. Previous studies using shoe and skin markers concluded that medially placed orthoses control/reduce foot eversion and tibial rotation. However, it is currently unknown if such orthoses also affect skeletal motion at the lower extremities. Methods. Intracortical Hofman pins with reflective marker triads were inserted under standard local anesthetic into the calcaneus and tibia of five healthy male subjects. The three-dimensional tibiocalcaneal rotations were determined using a joint coordinate system approach. Eversion (skeletal and shoe) and tibial rotation were calculated to study the foot orthoses effects. Results. Orthotic effects on eversion and tibial rotations were found to be small and unsystematic over all subjects. Differences between the subjects were significantly larger ( p < 0.01; up to 10°) than between the orthotic conditions (1–4°). Significant orthotic effects across subjects were found only for total internal tibial rotation; p < 0.05). Conclusions. This in vivo study showed that medially placed foot orthoses did not change tibiocalcaneal movement patterns substantially during the stance phase of running. Relevance Orthoses may have only small kinematic effects on the calcaneus and tibia (measured with bone pins) as well as on the shoes (measured with shoe markers) during running of normal subjects. Present results showed that orthotic effects were subject specific and unsystematic across conditions. It is speculated that orthotic effects during the stance phase of running may be mechanical as well as proprioceptive.