The sense of body ownership (i.e., the feeling that our body or its parts belong to us) plays a key role in bodily self-consciousness and is believed to stem from multisensory integration. The development of experimental paradigms that allow the controlled manipulation of body ownership in laboratory settings, such as the rubber hand illusion, provide an effective tool to investigate the malleability of the sense of body ownership and the boundaries distinguishing self and other. Neuroimaging studies on body ownership converge on the involvement of several cortical regions, including the premotor cortex and posterior parietal cortex. However, relatively less attention has been paid to subcortical structures that may also contribute to body ownership perception, such as the cerebellum and putamen. Here, on the basis of neuroimaging and neuropsychological observations, we provide an overview of relevant subcortical regions and consider their potential role in generating and maintaining a sense of ownership over the body. We also suggest novel avenues for future research targeting the role of subcortical regions in making sense of the body as our own.