Chronic exertional compartment syndrome (CECS) has been hypothesised, following clinical observations, to be the result of abnormal biomechanics predominantly at the ankle. Treatment of CECS through running re-education to correct these abnormalities has been reported to improve symptoms. However no primary research has been carried out to investigate the movement patterns of those with CECS. This study aimed to compare the running kinematics and muscle activity of cases with CECS and asymptomatic controls. 20 men with bilateral symptoms of CECS of the anterior compartment and 20 asymptomatic controls participated. Barefoot and shod running 3D kinematics and muscle activity of the left and right legs; and anthropometry were compared. Cases displayed less anterior trunk lean and less anterior pelvic tilt throughout the whole gait cycle and a more upright shank inclination angle during late swing (peak mean difference 3.5°, 4.1° and 7.3° respectively). Cases demonstrated greater step length and stance time, although this was not consistent across analyses. There were no consistent differences in Tibialis anterior or Gastrocnemius medialis muscle activity. Cases were heavier (mean difference 7.9kg, p=0.02) than controls with no differences in height (p>0.05) These differences only partially match the clinical observations previously described. However, no consistent differences were found at the ankle joint suggesting that current running re-education interventions which focus on adjusting ankle kinematics are not modifying pathological aspects of gait. The longer step length is a continuing theme in this population and as such may be a key component in the development of CECS.