The aim of this study was to determine the influence of motion control, neutral and cushioned running shoes upon inter-segmental foot kinematics. Twenty-eight active males completed one testing session, in which they ran in standardised motion control, neutral and cushioned running shoes on a treadmill at a self-selected pace (2.9 ± 0.6 m·s−1). Incisions were made within the shoes to enable the motion of the foot to be tracked using a motion analysis system and inter-segmental foot kinematics calculated using the Istituti Ortopedici Rizzoli foot model. Discrete parameters associated with midfoot–rearfoot, forefoot–rearfoot, forefoot–midfoot and medial longitudinal arch motion were compared between footwear conditions. Midfoot–rearfoot eversion upon initial contact and peak medial longitudinal arch angles (MLAA) were significantly lower in the motion control shoe compared to the neutral and cushioned shoes. The reductions in midfoot–rearfoot eversion and medial longitudinal arch deformation in the motion control running shoe may be due to increased medial posting and torsional control systems in this shoe. However, these changes in midfoot kinematics may be offset by significant increases in sagittal plane midfoot–rearfoot and forefoot–rearfoot range of motion, particularly during mid-stance.