Nanotechnology is a continuously rising field with different and varied purposes. Nanoparticles (NPs) are defined as particles between 1 and 100 nanometers in diameter, but within this classification larger particles can be incorporated up to 500 nm. Magnetic NPs (MNPs) are generally composed with magnetic elements such as nickel, cobalt and iron, and have the ability to be manipulated through a magnetic field. Recently, these have been the subject of numerous studies because their attractive properties for several potential applications. Among them, we can include its use for diagnosis and medical treatment (theragnosis). Due to their properties, MNPs could be used with the aim of developing immunomodulatory therapies and deal with infectious diseases, cancer, allergies, autoimmune diseases, etc. The use of MNPs provides a novel tool to manipulate the immune response towards a profile according to the proposed objectives. That is why this chapter describes the interaction of MNPs with the immune system as well as its possible applications in immunomodulatory therapies.