Synthesis of magnetic nanoparticles and magnetic nanoclusters was performed by the co-precipitation method or solvothermal synthesis, respectively, followed by oxidative polymerization of dopamine, resulting in a polydopamine (PDA) shell. The nanomaterials obtained were described using TEM, FTIR and magnetic measurements. For the first time, cyto- and genotoxicity studies of polydopamine-coated nanostructures were performed on cancer and normal cell lines, providing in-depth insight into the toxicity of such materials. The tests conducted, e.g. ROS, apoptosis and DNA double-break of the nanomaterials obtained revealed the low toxicity of these structures. Thus, these results prove the biocompatibility and low genotoxicity of these materials and provide new data on the toxicity of PDA-coated materials, which is of great importance for their biomedical application.