Although in recent years there has been an increasing amount of literature on nanotechnology and their clinical applications, it is still scarce a deep understanding of the interactions at the molecular levels between nanoparticles and cells. Studies demonstrating the underlying mechanisms of nanoparticles endocytosis, intracellular trafficking, and cellular processing are imperative to understand better how cells interact with those materials and their possible undesired effects, e.g. nanotoxicity. The rising awareness concerning nanoparticles applications and its interactions with the cellular environment is part of the new research field called Nanotoxicology. The cumulative knowledge in nanotoxicology will allow us to foresee toxic effects, establish regulations and limits for nanoparticles applications. In this work, we discuss the theoretical concepts about studying endocytosis and intracellular trafficking of nanoparticles. The nanoparticles-cell interactions are a multi-step process, which can be divided into nanoparticles' internalization, intracellular processing and triggering effects of nanomaterials on eukaryotic cells. Finally, we discuss the main techniques used to study this process: flow cytometry, use of endocytosis inhibitors and confocal microscopy.