The subthalamic nucleus (STN) is a key structure for somatic motor control via the basal ganglia. In the present study, we demonstrate that the STN of the macaque monkey has dual sets of body part representations. Each of the two separate portions of the STN is characterized with somatotopically arranged direct cortical inputs that are derived from the primary motor cortex (MI) and the supplementary motor area (SMA). The first set of body part representations is transformed from the MI to the lateral STN, whereas the second set is transformed from the SMA to the medial STN. Intracortical microstimulation mapping was carried out to guide paired injections of anterograde tracers into somatotopically corresponding regions of the MI and the SMA. We found that direct inputs from the MI were allocated mostly within the lateral half of the STN, whereas those from the SMA were distributed predominantly within its medial half. Of particular interest was that the arrangement of somatotopical representations from the SMA to the medial STN was reversed against the ordering of those from the MI to the lateral STN; the orofacial, forelimb, and hindlimb parts were represented from medial to lateral within the medial STN, whereas these body parts were represented, in the inverse order, mediolaterally within the lateral STN. Moreover, inputs from homotopical MI and SMA regions were found to converge only partially into the STN. The present findings could account for somatotopically specific involuntary movements manifested in hemiballism that is caused by destruction of the STN.