Protozoa as phagocytizing cells have been shown to integrate ngineered nanoparticles (NPs), while the mechanism, dynamics and extent of such uptake are unclear. Here our fluorescence microscopy data showed that CdSe/ZnS quantum dots (QDs) with primary size of 12 nm were readily phagocytized into the food vacuoles of Tetrahymena thermophila in a time- and dose-dependent manner. Twenty hours after the exposure to QDs in sublethal concentration the clearance of the QDs from the cells was incomplete suggesting that phagocytosis of QDs into food vacuoles was not the only pathway of uptake by T. thermophila. This was further proven by the results that the inhibition of phagocytosis did not lock the internalization of QDs into protozoans. This study provides a new insight into uptake and cellular trafficking of subtoxic oncentrations of nanoparticles that may, due to prolonged retention times in the cells, pose risks by potentially becoming available to higher trophic levels.