Siloxane surfactants containing tromethamol or carboxylate groups, with very good surface properties, are tested for the first time for biocompatibility using MTT cytotoxicity test. They are used for encapsulation of superparamagnetic iron oxide nanoparticles (SPION), and of a combination of these with nystatin as model un-soluble drug, in order to obtain stable aqueous dispersions. The initial magnetite and chromite nanoparticles have been synthesized previously by thermal decomposition thus being covered by dodecylamine and oleic acid. Their aqueous dispersions were obtained by physical methods using very low concentrations of siloxane surfactants, and were investigated by DLS, TEM, cryo-TEM and EDX. One such formulation was tested by MTT method and the results showed high cell viability. The nanoparticles covered with siloxane surfactants exhibited various types of morphology: individual particles, vesicle-like aggregates or composite particles, all having diameters roughly between 20 and 200. nm. The encapsulation of both SPION and nystatin confirmed our previous results on nystatin solubilization by encapsulation within the hydrophobic wall of surfactant vesicles.