The specific use of engineered nanostructures in biomedical applications has become very attractive, due to their ability to interface and target specific cells and tissues to execute their functions. Additionally, there is continuous progress in research on new nanostructures with unique optical, magnetic, catalytic and electrochemical properties that can be exploited for therapeutic or diagnostic methods. On the other hand, as nanostructures become widely used in many different applications, the unspecific exposure of humans to them is also unavoidable. Therefore, studying and understanding the toxicity of such materials are of increasing importance. Previously published reviews regarding the toxicological effects of nanostructures focus mostly on the cytotoxicity of nanoparticles and their internalization, activated signaling pathways and cellular response. Here, the most recent studies on the invitro cytotoxicity of NPs, nanowires and nanorods for biomedical applications are reviewed and divided into two parts. The first part considers nonmagnetic metallic and magnetic nanostructures, while, the second part covers carbon structures and semiconductors. The factors influencing the toxicity of these nanostructures are elaborated to help elucidate the effects of these nanomaterials on cells, which is a prerequisite for their safe clinical use.