Nanotechnology industry has begun its successful expansion into biomedicine. The capabilities of traditional imaging, delivery, and sensing devices were surpassed within a very short time by the nanoparticle tools. The nanoscale platforms have made significant progress in formulation preparations and achieved more precise treatment at a molecular level. Currently available dyes cannot provide a longterm imaging of numerous cell markers because of their photobleaching property. In comparison with previous micron-scale agents, nanoparticles are able to penetrate endothelial barriers to reach tumour sites. Nanotechnology is really promising but it surely still needs some time to develop so it is a question ‘when’, not ‘if’ nanoparticles will become a standard tool in biomedicine. So far we mostly discussed numerous positive features of nanoparticle therapeutics for cancer, but there are surely drawbacks present. Nanoparticle behaviour in the human body is not yet extensively studied and that is why nanoparticle toxicity makes a valid issue to concern about since nanoparticle size and surface properties allow them to reach the locations that are not reachable for larger particles. Different mechanisms such as binding to proteins in the blood or removal by macrophages can have its influence upon nanoparticle biodistribution. The latter phenomenon was investigated in rat blood–brain barrier using differently charged nanoparticles and it appeared that those that were highly charged altered the integrity of the blood–brain barrier irregardless of the charge sign. We can conclude that nanoparticle biocompatibility is yet to be fully defined. Nanostructure harmfulness was studied in animals and it turned out that toxicities vary significantly depending on the nanomaterial itself. Some nanoparticles described in this review have nevertheless passed strict toxicity tests and are already used in humans for years. The more biocompatibility data are available, the better we understand what is required to tune the properties of nanoparticles to ensure their safety for systemic use.