The brain's representation of hand position is critical for voluntary movement. Representation is multisensory, combining visual and proprioceptive cues. When these cues conflict, the brain recalibrates its unimodal estimates, shifting them closer together to compensate. Converging evidence from research in perception, behavior, and neurophysiology suggest that such updates to body representation are communicated to the motor system to keep hand movements accurate. We hypothesized that primary somatosensory cortex (SI) is crucial in this updating process due to its role in proprioception and connections with primary motor cortex. We tested this hypothesis in two experiments. We predicted that proprioceptive, but not visual, recalibration would be associated with change in short latency afferent inhibition (SAI), a measure of sensorimotor integration (influence of sensory input on motor output) (Expt. 1). We further predicted that modulating SI activity with repetitive transcranial magnetic stimulation (TMS) should affect recalibration of the proprioceptive estimate of hand position, but have no effect on the visual estimate or on the normal inverse relationship between proprioceptive and visual recalibration (Expt. 2). Our results are consistent with these predictions, supporting the idea that (1) SI is indeed a key region in facilitating motor system updates based on changes in body representation, and (2) this function is mediated by unisensory (proprioceptive) processing, separate from multisensory visuo-proprioceptive computations. Other aspects of the body representation (visual and multisensory) may be conveyed to the motor system via separate pathways, e.g. from posterior parietal regions to motor cortex.