There is a hypothesis that nanoparticles influence the development of microorganisms. The results exposed in some scientific papers reflects the aspects of influence of various nanoparticles (oxides of Au, Ag, Ti, Si, Zn) on the microbial cell, thus it can be noted that they can modify the development of microorganisms. According to some investigations, the mechanism of influence of nanoparticles of metal oxides on the microbial cell is complex and attracts changes in both the cell membrane and the cytoplasm. Proteins, due to their specific composition, play an important role in maintaining cellular integrity (cell wall proteins), catalysing different biochemical reactions. Under the action of various physical factors (ultrasound, radiation with different wavelengths, heat), chemical factors (acids, bases, various organic solvents) or mechanical (stirring), there is a phenomenon of change in the structure of proteins, which can be reversible or irreversible Generalizing information on the influence of nanoparticles on growth of microorganisms, the aim of this paper was to reveal the effects of Fe3O4 and ZnO nanoparticles on the process of biosynthesis of proteins at pigmented yeast strain Rhodosporidium toruloides CNMN-Y-30 (sinonim Rhodotorula gracilis). The results of the evaluation revealed different effects. Thus, Fe3O4 nanoparticles with dimension of 10 nm in concentrations from 0.5 to 30 mg / L of culture medium initiated a relatively moderate decrease in protein content in cell biomass with 12.0 ... 22.6 % compared to the control. The correlation ratio confirms the dependence of protein content values on those of Fe3O4 nanoparticles, the determination coefficient being strong (R2 = 0, 957). The other aspect of the influence of nanoparticles on protein biosynthesis in the yeast strain was observed with the application of 30 nm Fe3O4 nanoparticles. At the cultivation on the YPD medium with the addition of these nanoparticles in all experimental variants the increase in protein content in the yeast biomass constituted 14.1-23.8% compared to control. The research effectuated with ZnO nanoparticles <100 nm, applied at concentrations of 1-30 mg/L demonstrated that content of protein in the yeast biomass increases according to the applied concentrations. The maximum positive effect is specific for concentrations of 10 and 20 mg/L of nanoparticles. It can be mentioned that the correlation coefficient between the amount of protein accumulated and concentration of the nanoparticles applied in experiments is R² = 0.6484. Thus, analysing data obtained on the effects of nanoparticles of metal oxides on protein biosynthesis in pigmented yeast, it can be affirmed that their effect depends on the dimension and used concentration.