During breathing, the human thorax is expanded or contracted during inspiration and expiration. The morphology of the thorax seems to be determinant for endurance efforts. This study aims to analyse the variation of the thorax cross-sections during running exercises at different intensities and the influence of thorax morphology. Twenty-two athletes were captured using a motion capture system (13 reflective markers) while they performed an incremental running test. Three captures of each subject were performed at different intensities (45%, 70%, and 85% of HRR (heart rate reserve)) and three morphology groups were made by splitting their thoracic index. The results showed a significant increase in the anteroposterior and mediolateral cross-sections when the intensity of the exercise is also increased. No differences were found in the cross-sections due to the morphology of the thorax. However, subjects with a deeper thorax showed a different behaviour as they increased their anteroposterior cross-section during higher intensities, while flatter thorax subjects did not perform in the same way. This could be explained as compensation for the morphological disadvantage that a deeper ribcage shape suffers when developing endurance efforts. More investigations regarding thorax kinematics are needed for a better understanding of breathing disorders and physical activities.