The application of nanotechnology to the diagnosis and therapy of human diseases is already a reality and is causing a real revolution in how we design new therapies and vaccines. In this review we focus on the applications of nanotechnology in the field of autoimmunity. First, we review scenarios in which iron oxide nanoparticles have been used in the diagnosis of autoimmune diseases, mostly through magnetic resonance imaging (MRI), both in animal models and patients. Second, we discuss the potential of nanoparticles as an immunotherapeutic platform for autoimmune diseases, for now exclusively in pre-clinical models. Finally, we discuss the potential of this field to generate the 'perfect drug' with the capacity to report on its therapeutic efficacy in real time, that is, the birth of theranostics in autoimmunity.