Gene therapy offers an alternative for the treatment of diseases such as cancer or neurodegenerative diseases by replacing, introducing or inactivating genes in the patient. In this aspect, the use of nanoparticles as nucleic acid delivery systems that prevents its degradation and facilitates its incorporation into target cells has been a subject of intense study in recent years. Among them, magnetic nanoparticles (MNP) offer advantages as new alternatives for non-viral transfection, such as guiding the nanoparticle and its content through magnetic fields towards target organs, increasing the efficiency and reducing transfection times. The use of MNP carrying genetic information to achieve transfection by the application of magnetic fields is known as magnetofection. In most cases, superparamagnetic iron oxide nanoparticles (SPIONs) are used as vehicles which also contain a cationic organic coating to increase their stability, gene incorporation and interaction with cell membranes. Another field in which the application of these new technologies is gaining attention is in the development of DNA and RNA- based vaccines for immunization and immunotherapy. In the following chapter, the use of magnetofection for in vitro experiments as well as the study of in vivo vaccine assays or gene therapy using MNP as nucleic acid carriers, will be discussed.