Boron nitride nanotubes (BNNTs) represent an innovative and extremely intriguing class of nanomaterials. Thanks to their special chemical and physical characteristics, they have already found a large number of applications in the field of nanotechnology, and recent studies have shown their possible exploitation in the biomedical domain, both as nanocarriers and, more interestingly, as nanotransducers. In this review, the latest findings on the interactions between BNNTs and living systems are summarized, starting with the major issues of their stabilization in physiological media and their functionalization with bioactive molecules. Thereafter the biocompatibility data which have so far been made available are discussed, and the need for further extensive and standardized tests is highlighted. Finally, the appealing diagnostic and therapeutic opportunities offered by BNNT-based systems are described, envisioning the potential spill-over effects of such 'smart' and 'active' nanoparticles in nanomedicine.