Peculiar features of the modification of Fe3O4 magnetic nanoparticles (MNPs) obtained by co-precipitation from solutions of FeII and FeIII salts (10-nm MNPs) and by the gas-condensation method (30-nm MNPs) with 3-aminopropylsilane and then with L-lysine were studied. The chemically obtained MNPs possess more pronounced hydrophilic properties and therefore readily form stable aqueous colloidal solutions and can be loaded with a larger amount of L-Lys. However, samples based on the physically obtained MNPs were characterized by more efficient internalization and longer retention times by the NIH 3T3 cells. The results obtained can be used in the design of novel nanomaterials for magnetic cell labeling.