With the development of nanotechnology, there are growing concerns about biological effects and biosafety of engineered nanomaterials. On the other hand, nanoparticles are widely used in medical fields based on their novel interactions with biological entities. However, there are still a lot of challenges to establish systematic knowledge about nanotoxicology and develop biologically safer biomedical materials due to the variety of factors determining their biomedical effects and nanotoxicity. Understanding the interactions of engineered nanomaterials with the biological entities becomes crucial to the further development of nanoscience and nanotechnology. In the past decade, colleagues in our laboratory intensively studied the toxic properties of various kinds of nanomaterials and their chemical mechanisms. In this paper we review the recent advance in the research on the biological effects of engineered nanomaterials and nanosafety issue, by focusing on the studies about representative nanomaterials in our laboratory.