In sports, there is a constant discussion about the hyper-pronation and supination of the foot during loading and its relation to injuries or discomfort. The purpose of the present study was to investigate the possible differences in the subtalar joint in the midstance phase of running, between individuals with Pes Planus and Pes Cavus, after 5 min and 45 min of running. Thirty-four subjects, meeting the requirements for Pes Planus (30 feet) and Pes Cavus (35 feet), according to the criteria for Medial Longitudinal Arch-angle, were included in the study. The calcaneal vertical angle, representing the eversion/inversion of the subtalar joint, was measured using with two-dimensional digital analysis and Dartfish Software with the subjects running barefoot on a treadmill, before and after 45 min of outside running wearing shoes. Both individuals with Pes Cavus and Pes Planus showed a significant increase in the calcaneal eversion (P<0.05) after 45 min of running. Between the groups, there was a significantly greater eversion of the Pes Planus, on the right foot, after 45 min of running (P<0.05) compared to the Pes Cavus. The effect of fatigue evident in the present study suggests that further biomechanical research should be considered when exposing the foot to the repetitive nature of running, conditions most likely responsible for the overrepresented overuse injuries among runners.