Barefoot running kinematics has been described to vary considerably from shod running. However, previous investigations were typically based on externally mounted shoe and/or skin markers, which have been shown to overestimate skeletal movements. Thus, the purpose of this study was to compare calcaneal and tibial movements of barefoot versus shod running using skeletal markers. Intracortical bone pins with reflective marker triads were inserted under standard local anesthetic into the calcaneus and tibia of five healthy male subjects. The subjects ran barefoot, with a normal shoe, with three shoe soles and two orthotic modifications. The three-dimensional tibiocalcaneal rotations were determined using a joint coordinate system approach. Test variables were defined for eversion and tibial rotation. The results showed that the differences in bone movements between barefoot and shod running were small and unsystematic (mean effects being less than 2 degrees ) compared with the differences between the subjects (up to 10 degrees ). However, differences may occur during midstance when extreme shoe modifications (i.e. posterior orthosis) are used. It is concluded that calcaneal and tibial movement patterns do not differ substantially between barefoot and shod running, and that the effects of these interventions are subject specific. The result of this in vivo study contrasts with previous investigations using skin and shoe mounted markers and suggests that these discrepancies may be the result of the overestimation with externally mounted markers.