In the frame of the European project NanoValid, potential candidates of reference nanomaterials are manufactured and systematically characterized in particular with respect to their morphology (shape, size and size distribution). In this study, by exploiting the transmission operation mode in a high‐resolution SEM, known as transmission SEM, the potential of this methodical approach is demonstrated by means of representative examples of nanoparticles. The method enables quick and accurate morphological inspection and systematic characterization. Energy dispersive X‐ray spectroscopy imaging of single nanoparticles by using the transmission mode is demonstrated as feasible, too. Copyright © 2014 John Wiley & Sons, Ltd.