Nanomaterials are expected to have a significant impact on medicine, although they still need to overcome several challenges before they are widely used. Understanding the molecular interaction of nanomaterials in the context of the cellular environment is crucial for the success of nanomaterials. Therefore, mechanisms responsible for nanomaterial internalization have attracted great attention in the scientific community. These mechanisms greatly impact intracellular trafficking and cellular processing of nanomaterials. Here we discuss the major endocytic pathways by which nanomaterials can be internalized by cells, such as clathrin-mediated endocytosis, caveolae-mediated endocytosis, macropinocytosis, and clathrin-and caveolae-independent endocytosis. In addition, intracellular routing, metabolism of nanomaterials, and undesirable effects of nanotoxicology are discussed. Finally, the role of in vitro studies to evaluate the potential toxic effects of nanomaterials was critically analyzed.