The use of nanoparticles with the ability to transport drugs in a selective and controllable manner directly to diseased tissues and cells has improved the therapeutic arsenal for addressing unmet clinical situations. In recent years, a vast number of nanocarriers with inorganic, organic, hybrid and even biological nature have been developed especially for their application in the oncology field. The exponential growth in the field of nanomedicine would not have been possible without the also-rapid expansion of electron microscopy techniques, which allow a more precise observation of nanometric objects. The use of these techniques provides a better understanding of the key parameters which rule the nanoparticles' synthesis and behavior. In this review, the recent advances made in the application of inorganic nanoparticles to clinical uses and the role which electron microscopy has played are presented.