Functional magnetic resonance imaging (fMRI) was used (1) to describe the pattern of whole brain activity during motion of isolated joints of the lower limb, (2) to examine the somatotopic organization of lower limb joint representations in the primary sensorimotor cortex and the anterior lobe of the cerebellum and 3) to quantify the degree of overlap between these lower limb joint activations. Eighteen healthy, right leg dominant volunteers participated in a motor block-design study, performing repetitive knee, ankle and toes flexion/extension movements. In order to relate lower limb joints activation to the well-described patterns of finger movement, serial finger-to-thumb opposition was also assessed. All movements were auditory paced at 72 beats/min (1.2 Hz). Isolated lower limb joints movement activated a distributed sensorimotor network, including primary and non-primary sensorimotor areas. Although a large overlap was evident in primary sensorimotor cortex (SM1) and cerebellum representations of the three lower limb joints, a somatotopic arrangement was recognizable with reference to center of mass coordinates of each individual joint in the above areas. Detection of active brain regions during movement of the lower limb joints is feasible with fMRI although a carefully optimized methodology protocol is required.