The advent of micro/nanomotors (MNMs) has shed light on the innovation of active biomedical systems or devices that might bring revolutionary solutions to traditional biomedical strategies. In spite of development beyond expectation over the last decade with a fair number of proof-of-concept demonstrations, the in vivo practical application of MNMs for clinical use is still in its infancy. The biocompatibility of MNMs is the first consideration before realizing practicality, taking into account the complicated interactions between the self-propelled MNMs and biological systems. Therefore, in this review, we focused on the biocompatibility of MNMs with regard to the fabrication materials and propulsion mechanisms by means of in-depth discussions on the advantages and limitations of MNMs for operating under physiological conditions. The future prospective and suggestions on the development of MNMs toward practical biomedical applications will also be proposed.