Zr-based bulk metallic glasses (BMGs) are a new type of metallic materials with disordered atomic structure that exhibit high strength and high elastic strain, relatively low Young's modulus, and excellent corrosion resistance and biocompatibility. The combination of these unique properties makes the Zr-based BMGs very promising for biomaterials applications. In this review article, the authors give an overview of the recent progress in the study of biocompatibility of Zr-based BMGs, especially the relevant work that has been done in the metallic glasses group in Huazhong University of Science and Technology (HUST), including the development of Ni-free Zr-based BMGs, the mechanical and wear properties, the bio-corrosion resistance, the in vitro and in vivo biocompatibility and the bioactive surface modification of these newly developed BMGs.