One of the frontier of nanoscience is undoubtedly represented by the use of nanotechnologies in the pharmaceutical research. During the last decades a big family of nanostructures that have a surface-acting action, such as NanoParticles (NPs), lipid nanocarriers and many more, have been developed to be used as Drug Delivery Systems (DDSs). However, these nanocarriers opened also new frontiers in nanometrology, requiring an accurate morphological characterization, near atomic resolution, before they are really available to clinicians to ascertain their elemental composition, to exclude the presence of contaminants introduced during the synthesis procedure and to ensure biocompatibility. Classical Transmission (TEM) and Scanning Electron Microscopy (SEM) techniques frequently have to be adapted for an accurate analysis of formulation morphology, especially in case of hydrated colloidal systems. Specific techniques such as environmental scanning microscopy and/or cryo preparation are required for their investigation. Analytical Electron Microscopy (AEM) techniques such as Electron Energy-Loss Spectroscopy (EELS) or Energy-Dispersive X-ray Spectroscopy (EDXS) are additional assets to determine the elemental composition of the systems. Here we will discuss the importance of Electron Microscopy (EM) as a reliable tool in the pharmaceutical research of the 21(st) century, focalizing our attention on advantages and limitations of different kind of NPs (in particular silver and carbon NPs, cubosomes) and vesicles (liposomes and niosomes).