Background: Many toxicological studies on silica nanoparticles (NPs) have been reported, however, the literature often shows various conclusions concerning the same material. This is mainly due to a lack of sufficient NPs characterization as synthesized as well as in operando. Many characteristics of NPs may be affected by the chemistry of their surroundings and the presence of inorganic and biological moieties. Consequently, understanding the behavior of NPs at the time of toxicological assay may play a crucial role in the interpretation of its results.The present study examines changes in properties of differently functionalized fluorescent 50 nm silica NPs in a variety of environments and assesses their ability to absorb proteins from cell culture medium containing either bovine or human serum. Methods: The colloidal stability depending on surface functionalization of NPs, their concentration and time of exposure was investigated in water, standard biological buffers, and cell culture media by dynamic light scattering (DLS), zeta potential measurements and transmission electron microscopy (TEM). Interactions of the particles with biological media were investigated by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) in bovine and human serum, and extracted proteins were assessed using matrix-assisted laser desorption/ionization-time of flight technique (MALDI-TOF).Results: It was recognized that all of the studied silica NPs tended to agglomerate after relatively short time in buffers and biological media. The agglomeration depended not only on the NPs functionalization but also on their concentration and the incubation time. Agglomeration was much diminished in a medium containing serum. The protein corona formation depended on time and functionalization of NP, and varied significantly in different types of serum.Conclusions: Surface charge, ionic strength and biological molecules alter the properties of silica NPs and potentially affect their biological effects. The NPs surface in bovine serum and in human serum varies significantly, and it changes with incubation time. Consequently, the human serum, rather than the animal serum, should be used while conducting in vitro or in vivo studies concerning humans. Moreover, there is a need to pre-incubate NPs in the serum to control the composition of the bio-nano-composite that would be present in the human body.