Pathogens and vaccines stimulate the immune system through an intricate and elaborate network of specialized cells and organs. Immune activation triggers several biological activities that require spatial and dynamic coordination. These activities range from recognition of pathogen-derived factors to cell intercommunication to cell differentiation. Systems biology approaches provide a comprehensive way of dissecting the complex interactions within these processes, and can lead to a better understanding of vaccine-induced immunity and disease pathogenesis. In recent years, systems biology has been successfully applied in analyzing the immune response to a wide range of vaccines and infectious agents. However, dealing with the large amount of data generated from high-throughput techniques and the inherent complexity of the immune system represent major computational and biological challenges. This chapter highlights the recent technological and methodological advances in the field and shows how systems biology can be applied to unraveling novel insights into the molecular mechanisms of immunity.