Nowadays nanostructures are more and more often designed as carriers for drug delivery, especially to improve the drug pharmacokinetics and pharmacodynamics. Numerous kinds of nanostructures are considered a good prospect for medical applications thanks to their small size, acceptable biocompatibility and toxicity. Due to the fact that nanotechnology is a new field of science, every nano-scale product must be thoroughly examined regarding its toxicity to the human body. This study provides new insights into effects of exposing endothelial cells to the selected nanostructures. Dendrimers of the fourth generation (PAMAMs), multi-walled carbon nanotubes (MWCNTs) and silver nanoparticles (SNPs) were used to evaluate nanostructures influence on endothelial cells in vitro. The nanostructures were evaluated via transmission electron microscopy and dynamic light scattering technique. The cells previously exposed to the nanostructures were observed and analyzed via the atomic force microscopy and scanning electron microscopy to obtain a quantitative evaluation of the cells morphology. The presence of multi-walled carbon nanotubes and silver nanoparticles on the cells surface was confirmed by the scanning electron microscopy. Our results confirm that the surface association and/or uptake of nanostructures by the cells resulting from physicochemical and biological processes, affect the cells morphology. Morphological changes can be induced by the membrane proteins interaction with nanomaterials, which trigger a sequence of intracellular biological processes.