The nanotechnology revolution offers many expectations for the improvement of medicine treatments. At present, nanomedicine (NM) development is hampered by methodological barriers for a better characterization and a wider understanding of their in vivo behavior. While regulatory agencies setup guidelines to support NM translation from bench to bedside, the gap is still hardly overcome by main nanomedicines. One lever for filling this gap is a better characterization, thus increasing the global knowledge about the NM itself but also validate the confidence in terms of batch to batch reproducibility of such complex nano-objects. Here, we review the current methodologies routinely used for clinical release of nanomedicine batches in compliance with official guidelines. We confront them to the extreme sharpness of biological systems and finally discuss future possible orientations for a better characterization of NMs, needed to bridge the gap between physicochemical properties and biological fate.