INTRODUCTION: The aim of this study was to investigate possible differences in the organisation of the motor cortex in people with knee osteoarthritis (OA) and whether there is an association between cortical organisation and accuracy of a motor task. METHODS: fMRI data were collected while 11 participants with moderate/severe right knee OA (6 male, 69 +/- 6 (mean +/- SD) years) and seven asymptomatic controls (5 male, 64 +/- 6 years) performed three visually guided, variable force, force matching motor tasks involving isolated isometric muscle contractions of: 1) quadriceps (knee), 2) tibialis anterior (ankle) and, 3) finger/thumb flexor (hand) muscles. fMRI data were used to map the loci of peak activation in the motor cortex during the three tasks and to assess whether there were differences in the organisation of the motor cortex between the groups for the three motor tasks. Root mean square of the difference between target and generated forces during muscle contraction quantified task accuracy. RESULTS: A 4.1 mm anterior shift in the representation of the knee (p = 0.03) and swap of the relative position of the knee and ankle representations in the motor cortex (p = 0.003) were found in people with knee OA. Poorer performance of the knee task was associated with more anterior placement of motor cortex loci in people with (p = 0.05) and without (p = 0.02) knee OA. CONCLUSIONS: Differences in the organisation of the motor cortex in knee OA was demonstrated in relation to performance of knee and ankle motor tasks and was related to quality of performance of the knee motor task. These results highlight the possible mechanistic link between cortical changes and modified motor behavior in people with knee OA.