Recent advances in nanotechnology have transformed the biomedicine field, in which the use of engineered nanomaterials (ENMs) has provided the foundation for novel applications. For this reason, the number of ENMs has increased rapidly, and here we provide a classification of ENMs based on chemical composition and biomedical applications, which include regenerative medicine, delivery systems, theranostics, and therapy. These have been identified as the most advanced and promising areas for further studies with humans. In addition, we discuss possible side effects related to ENM uses. We identify carbon, metal, and metal oxides as the most versatile ENM material groups, used in bone and neuronal regenerative medicine, thermal therapy, theranostics, drug delivery, gene therapy, and biosensors. However, the majority of drugs approved by the U.S. Food and Drug Administration (FDA) are lipid-based ENMs. We conclude that biomedical applications of ENMs offer potential benefits while side effects are mainly associated with occupational exposure. Finally, we suggest that in the future, nanocomposites, subnanometric structures, and biodegradable and biocorona formation could be used to improve the biomedical field by focusing on infectious diseases, early detection, and precision medicine.