The purpose of this study was to examine the knee and ankle joint stiffness and negative joint work during running when participants utilised their preferred and non-preferred footfall pattern. A total of 40 healthy, young runners (20 habitual forefoot (FF) and 20 habitual rearfoot (RF) runners) served as participants in this study. Three-dimensional data were obtained using a motion capture system and a force platform. The participants completed over-ground trials in each of two conditions: 1. their natural footfall pattern; and 2. their non-preferred footfall pattern. Joint stiffness was calculated by the ratio of the change in joint moment and the change in joint angle during the energy absorption phase of support. Negative joint work was calculated as the integral of the joint power-time curve during the same time interval. It was observed that joint stiffness was different between the footfall patterns but similar for both groups within a footfall pattern. A stiffer knee and a more compliant ankle were found in the FF pattern and the opposite in the RF pattern. Negative work was greater in the ankle and less in the knee in the FF pattern and the reverse in the RF pattern. We conclude that runners, in the short term, can alter their footfall pattern. However, there is a re-organisation of the control strategy of the joint when changing from a FF to a RF pattern. This re-organisation suggests that there is a possible difference in the types of injuries that may be sustained between the FF and the RF footfall patterns.