Silver nanoparticles (AgNPs) are being manufactured quickly and in large quantities due to their exeptional physical, chemical and biological properties that increase the efficiency of antimicrobial action of silver. However, because of their large surface area to volume ratio, AgNPs are highly reactive and subjected to silver ions (Ag+) release which potentially increases their toxicity. In this graduation thesis the impact of AgNPs stabilized with different coatings (citrate, CTAB, PVP) and the impact of AgNO3 on onion root morphology and the expression of total soluble proteins were examined. Significant morphological changes in the ultrastructure of onion root cells were not observed in this research, but it was found that AgNPs entered those cells and accumulated in them. Changes in protein profiles of differently treated onion roots were analyzed with two-dimensional gel electrophoresis and mass spectrometry was used to identify proteins with different expressions. It was found that both forms of silver caused different changes in protein profile of root cells; they increased expression of proteins included in carbohydrate metabolism, plant mechanisms against stress, plant growth and development, processes associated with growth hormones, cellular respiration and regulation of transcription and decreased expression of proteins that play a role in transport, defence, protein synthesis and chromosome stability. The results showed that silver ions and AgNPs stabilized with three different organic coatings have mutually different effects on root size/thicknes and primarily cause the increased expression of the proteins in onion root cells.