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This panel-randomized intervention trial was designed to examine the effect of a motor control training program for elite Australian Football League players with and without low back pain (LBP).The outcome measures included cross-sectional area (CSA) and symmetry of multifidus, quadratus lumborum, and psoas muscles and the change in CSA of the trunk in response to an abdominal drawing-in task. These measures of muscle size and function were performed using magnetic resonance imaging. Availability of players for competition games was used to assess the effect of the intervention on the occurrence of injuries. The motor control program involved performance of voluntary contractions of the multifidus and transversus abdominis muscles while receiving feedback from ultrasound imaging. Because all players were to receive the intervention, the trial was delivered as a stepped-wedge design with three treatment arms (a 15-wk intervention, a 8-wk intervention, and a waitlist control who received a 7-wk intervention toward the end of the playing season). Players participated in a Pilates program when they were not receiving the intervention.The intervention program was associated with an increase in multifidus muscle size relative to results in the control group. The program was also associated with an improved ability to draw-in the abdominal wall. Intervention was commensurate with an increase in availability for games and a high level of perceived benefit.The motor control program delivered to elite footballers was effective, with demonstrated changes in the size and control of the targeted muscles. In this study, footballers who received the intervention early in the season missed fewer games because of injury than those who received it late in the playing season.