The administration route of vaccines and the subsequent targeting towards the immune system can strongly influence the quality and acceptability of vaccines. Vaccination via the skin or the mucosae has potential advantages over classical injections but is not routinely used because of inefficient delivery and immune stimulation. To deliver vaccines to the skin, we are developing microneedle-based concepts. For mucosal vaccination we are exploring nasal, sublingual and pulmonary routes in preclinical models. We use antigen-loaded nanoparticles to target antigens to different compartments of the immune system and to induce the desired type of immune response (e.g., humoral, cellular, tolerogenic). In vitro cell culture and tissue models are being developed and applied to study the interactions between these delivery systems with the absorbing membranes and relevant cells. Analytical tools to characterize our antigens and vaccine delivery systems range from physico-chemical to cell-based assays. For in vivo studies we are increasingly using systems biology approaches like transcriptomic and proteomic techniques.