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The increasing interest in the use of magnetic fluids (MF) for biomedical applications demand deeper knowledge related to its effects on living beings. Previous biological studies on a magnetic fluid (MF) sample based on dextran-coated magnetite nanoparticles (Dex-MF) performed by magnetic resonance and light microscopy showed that the magnetic nanoparticles (MNPs) were concentrated in the liver and spleen of mice. In the present study aspects related to MNP uptake, MNP processing, and possible ultrastructural alterations after long-term retention in the body were studied from 5 minutes up to 2 months after injection of Dex-MF sample using transmission electron microscopy. The results evidenced the importance of using the TEM in the investigation of dextran-coated magnetite nanoparticles effects on mice. Electron microscopy showed the process of capture of Dex-MF nanoparticles from the blood, the formation of phagolysosomes, and the tissues and cells involved in the iron metabolism. Microscopic analysis also showed that although MNPs or the extra iron released from them are long-term retained in the organism, no ultrastructural alteration is induced until two months after Dex-MF administration, evidencing the MF biocompatibility and utility for biomedical applications.