Vaccines based on attenuated or killed viruses and bacteria are highly effective in preventing infection with a range of pathogens, but can have safety issues. Therefore, a move is underway toward the development of subunit vaccines based on recombinant proteins or naked DNA. However, protein subunit vaccines are typically poorly immunogenic when administered alone and therefore require coadministration with adjuvants to boost the immune response. For many decades, very little progress was made in understanding the mechanism of action of adjuvants, but recently several significant breakthroughs have occurred in this area. The binding of pathogen-derived molecules to different immune sensors, including Toll-like receptors (TLR), nucleotide-binding oligomerization domain-like receptors (NLR), and retinoic acid-inducible gene (RIG)-1-like receptors (RLR), activates important innate immune pathways and provides not only an understanding of how current vaccines and adjuvants work, but also potential targets for novel adjuvant development.