CdSe and CdTe-based semiconductor fluorescent nanocrystals, also called quantum dots (QDs), attract the attention of biologists due to their wide range of emission in a visible light interval, high fluorescence quantum yield and photostability. However, their application is limited because of possible toxicity of cadmium. Indeed, there is a probability of metal leakage from QDs cores as a result of damage of both inorganic and organic layers of shells covering QDs. An alternative to cadmium QDs could be nanostructures having as a core, for example, non-toxical indium phosphide (InP), also emitting in the visible region of the spectrum. At present, there is few works on the use of these particles in biology. In this study, a comparative analysis of the spectral-luminescent properties of two InP/ZnS-QDs samples coated with PEG carrying- COOH or -NH2 functional groups was performed. The obtained data were compared with the characteristics of CdSe/ZnS-QDs coated with PEG. The photophysical properties of all QDs in aqueous solution corresponded to the information claimed by manufacturers, but the fluorescence quantum yield of InP-based nanoparticles was found to be lower than that of CdSe-QDs. We also show that the photoluminescence of all types of QDs at pH 4.0 was lower than at pH 7.4, while the decrease in fluorescence intensity was minimal in the case of QDs-PEG-COOH. Studying the uptake of all three types of QDs by J774 macrophages, we found that the fluorescence spectra of internalized QDs do not change in comparison with those in solution. All three types of QDs after 24 hours of incubation were accumulated in the cells, but while QDs-NH2 and QDs without reactive groups were detected mainly in vesicular-like discrete structures, the QDs-COOH were diffusely distributed throughout the cytoplasm. This fact indicates different mechanisms of interaction with cell membranes. In nonphagocytic HeLa cells all types of QDs behaved similarly, but the overall level of cells fluorescence was much lower. This may be due to both reduced nonspecific uptake and possible quenching of QDs fluorescence in acidic endolysosomes. Cytofluorimetric analysis of propidium iodide accumulation showed that after 24 hours incubation with all studied types of QDs as well as in control (no QDs), the proportion of dead HeLa cells did not exceed 10%. Thus, it has been demonstrated that non-toxic InP-based QDs can be used as an effective tool for biological research.