Since magnetic particles have unique features, the development of a variety of medical applications has been possible. The most unique feature of magnetic particles is their reaction to a magnetic force, and this feature has been utilized in applications such as drug targeting and bioseparation including cell sorting. Recently, magnetic nanoparticles have attracted attention because of their potential as contrast agents for magnetic resonance imaging (MRI) and heating mediators for cancer therapy (hyperthermia). Magnetite cationic liposomes (MCLs), one of the groups of cationic magnetic particles, can be used as carriers to introduce magnetite nanoparticles into target cells since their positively charged surface interacts with the negatively charged cell surface; furthermore, they find applications to hyperthermic treatments. Magnetite nanoparticles conjugated with antibodies (antibody-conjugated magnetoliposomes, AMLs) are also applied to hyperthermia and have enabled tumor-specific contrast enhancement in MRI via systemic administration. Since magnetic nanoparticles are attracted to a high magnetic flux density, it is possible to manipulate cells labeled with magnetic nanoparticles using magnets; this feature has been applied in tissue engineering. Magnetic force and MCLs were used to construct multilayered cell structures and a heterotypic layered 3D coculture system. Thus, the applications of these functionalized magnetic nanoparticles with their unique features will further improve medical techniques.