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The synthesis of magnetic materials such as nanostructured iron oxide has been intensively researched due to their broad applications in biomedicine. As these nanoparticles have high specific surface area, they are very reactive and can aggregate easily, and biodegrade when exposed to biological systems. Mesoporous silica is often employed as support matrix to protect the magnetic functional component, avoiding undesirable effects. In this context, this review describes various syntheses of silica-coated iron oxide nanoparticles, and their use in applications such as bioseparation, magnetic resonance imaging, hyperthermia and drug delivery systems showing the growing interest of these materials in biological area.