DNA vaccination represents a new milestone in our technological efforts to avoid infectious diseases. Although this method of vaccination has had success in providing protection in animals, these vaccines suffer from low immunogenicity in humans. Questions remain over the molecular mechanism of DNA vaccination, the best ways in which to safely increase vaccine reactogenecity, and what biomarkers can be used as correlates of protection. Systems vaccinology, which utilizes modern experimental and computational approaches to provide an integrated view of the vaccination process, offers the potential to answer these questions. In this review we discuss the current tools utilized in systems vaccinology, the ways in which they have and can be applied to DNA vaccinology, and challenges faced in the field.