Recent developments in wearable and wireless sensor technology allow for a continuous three dimensional analysis of running mechanics in the sport specific setting. The present study is the first to demonstrate the possibility of analyzing three dimensional (3D) running mechanics continuously, by means of inertial magnetic measurement units, to objectify changes in mechanics over the course of a marathon. Three well trained male distance runners ran a marathon while equipped with inertial magnetic measurement units on trunk, pelvis, upper legs, lower legs and feet to obtain a 3D view of running mechanics and to asses changes in running mechanics over the course of a marathon. Data were continuously recorded during the entire 42.2 km (26.2 Miles) of the Marathon. Data from the individual sensors were transmitted wirelessly to a receiver, mounted on the handlebar of an accompanying cyclist. Anatomical calibration was performed using both static and dynamic procedures and sensor orientations were thus converted to body segment orientations by means of transformation matrices obtained from the segment calibration. Joint angle (hip, knee and ankle) trajectories as well as center of mass (COM) trajectory and acceleration were derived from the sensor data after segment calibration. Data were collected and repeated measures one way ANOVA׳s, with Tukey post-hoc test, were used to statistically analyze differences between the defined kinematic parameters (max hip angle, peak knee flexion at mid-stance and at mid-swing, ankle angle at initial contact and COM vertical displacement and acceleration), averaged over 100 strides, between the first and the last stages (8 and 40 km) of the marathon. Significant changes in running mechanics were witnessed between the first and the last stage of the marathon. This study showed the possibility of performing a 3D kinematic analysis of the running technique, in the sport specific setting, by using inertial magnetic measurement units. For the three runners analyzed, significant changes were observed in running mechanics over the course of a marathon. The present measurement technique therefore allows for more in-depth study of running mechanics outside the laboratory setting.