To understand how nanoparticles (NPs) interact with biological barriers and to ensure they maintain their integrity over time, it is crucial to study their in vivo pharmacokinetic (PK) profiles. Many methods of tracking have been used to describe the in vivo fate of NPs and to evaluate their PKs and structural integrity. However, they do not deliver the same level of information and this may cause misinterpretations. Here, the authors review and discuss the different methods for in vivo tracking of organic NPs. Among them, Förster resonance energy transfer (FRET) presents great potential to track NPs' integrity. However, FRET still requires validated methods to extract and quantify NPs in biological fluids and tissues.