Abstract During the last decade, research into nanotechnology has begun to merge with immunotherapy. Nanoparticles present multiple advantages when used as adjuvants in vaccines, or for as drug-delivery systems for immunostimulant or immunosuppressive compounds. A rational design of the formulation allows the development of nanosystems targeted to each demand. Here, we review how the physicochemical properties of the system (e.g., size, surface charge, shape, surface morphology, flexibility/elastic modulus, and chemical functionalization) influence the interaction between particles and cells, and their cytocompatibility and immunological properties. In a successful nanovaccine formulation, the choice of adjuvant and the selection of the antigen position on the particles define the type of the immunological response produced. Moreover, in the discovery process, reliable and established in vitro models are needed to screen the initial formulations allowing for a careful choice and further optimization. Finally, we present the animal models currently employed for the in vivo evaluation of nanoparticles for immunomodulatory applications, ranging from cancer models to models of autoimmune diseases.