The use of vaccines has led to tremendous decreases in disease burdens across the world. Many challenges remain in expanding vaccine coverage to new pathogens, however, a struggle further hampered by a lack of understanding into many of the fundamental processes through which vaccines elicit robust immunity. In this review we cover recent advances in the field of innate immunity and vaccinology that offer new insights into the reasons some vaccines may succeed or fail. We begin with the secreted cytokines that can influence the nature of the adaptive immune response, and how these may be tuned with the use of particular adjuvants. From there we cover dendritic cells, perhaps the key cell at the interface between innate and adaptive immunity. We discuss mechanisms for targeting specific subsets of dendritic cells, and the effects of this targeting. We further discuss additional modifications of the vaccine formulation to enhance interactions with innate immunity, including phagocytocis and antigen presentation. Finally, we step back to review recent advances in systems biology, and the ability of these new tools to provide deeper understanding of innate immune functions. We hope that this review will provide researchers with access to a breadth and depth of recent work that will allow for the rational design of novel vaccines to combat the most serious infectious diseases of today and tomorrow.