It is important to obtain a better understanding of the uptake, trafficking, pharmacokinetics, clearance, and role of nanomaterials in biological systems, so that their possible undesirable effects can be avoided. A number of metallic or metal-containing nanomaterials, such as gold nanoparticles and nanorods, quantum dots, iron oxides nanoparticles, and endohedral metallofullerenes, have already been or will soon become very promising for biomedical applications. This review presents a summary of currently available data on the fate and toxicity of these metallic or metal-containing nanoparticles based on animal studies. Several issues regarding the nanotoxicity assessment and future directions on the study of the fate of these nanoparticles are also proposed.