To investigate the short-term effects of recreational running on the deformation of knee articular cartilage and to examine the relationship between changes in knee cartilage volume and biomechanical modulators of knee joint load. Twenty healthy volunteers participated in a two phase cross-sectional study. Session 1 involved Magnetic Resonance Imaging (MRI) of femoral and tibial cartilage volumes prior to and following a 30 min period of relaxed sitting, which was directly followed by a recreational run of 5000 steps. Subsequently, all participants undertook a laboratory study of their running gait to compare biomechanical derived measures of knee joint loading with changes in cartilage volume. Estimates of knee joint load were determined using a rigid-link segment, dynamic biomechanical model of the lower limbs and a simplified muscle model. Running resulted in significant deformation of the medial (5.3%, P<0.01) and lateral femoral cartilage (4.0%, P<0.05) and lateral aspect of the tibial cartilage (5.7%, P<0.01), with no significant differences between genders. Maximum compression stress was significantly correlated with percentage changes in lateral femoral cartilage volume (r(2)=0.456, P<0.05). No other biomechanical variables correlated with volume changes. Limited evidence was found linking biomechanical measures of knee joint loading and observed short-term deformation of knee articular cartilage volume following running. Further enhancement of knee muscle modelling and analysis of stress distribution across cartilage are needed if we are to fully understand the contribution of biomechanical factors to knee joint loading and the pathogenesis of knee osteoarthritis (OA).