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Abstract The widely used rubber hand illusion (RHI) paradigm provides insight into how the brain manages conflicting multisensory information regarding bodily self-consciousness. Previous functional neuroimaging studies have revealed that the feeling of body ownership is linked to activity in the premotor cortex, the intraparietal areas, the occipitotemporal cortex, and the insula. The current study investigated whether the individual differences in the sensation of body ownership over a rubber hand, as measured by subjective report and the proprioceptive drift, are associated with structural brain differences in terms of cortical thickness in 67 healthy young adults. We found that individual differences measured by the subjective report of body ownership are associated with the cortical thickness in the somatosensory regions, the temporo-parietal junction, the intraparietal areas, and the occipitotemporal cortex, while the proprioceptive drift is linked to the premotor area and the anterior cingulate cortex. These results are in line with functional neuroimaging studies indicating that these areas are indeed involved in processes such as cognitive-affective perspective taking, visual processing of the body, and the experience of body ownership and bodily awareness. Consequently, these individual differences in the sensation of body ownership are pronounced in both functional and structural differences.