In this work, the effect of a cell culture medium on the integrity of mesoporous silica shell of gold-core nanoparticles (Au@SiO2 NPs) and their behavior in cells of HeLa, MDA-MB and BT cultures were studied using the method of transmission electron microscopy. It was shown that degradation of Au@SiO2 NPs takes place in the culture medium. The presence of the cells and serum does not influence on the process of the mesoporous silica layer degradation. The presence of both damaged and undamaged NPs in endosomes and lysosomes is related to different time of NPs’ location outside of the cell, i.e. in culture medium. The analysis of the cell ultrastructure leads to a conclusion that the internal conditions in endosomes/lysosomes do not influence on the integrity of Au@SiO2 NPs.