Genome-based reverse vaccinology (RV) is a multi-step experimental strategy which starts from in silico analysis of whole genome sequences, from which vaccine candidates can be selected by using bioinformatic algorithms to identify putative protective antigens. In this review, we examine the current state of genome-based RV-engineered vaccines and future applications. The first product of genome-based RV is Bexsero(®), a vaccine developed for preventing Neisseria meningitidis serogroup B infection, and the strategy is currently being used for the development of new vaccines for other obdurate and emerging bacterial diseases. Improved sequencing technologies and the ongoing whole-genome sequence analyses of helminths, protozoa, and ectoparasites also currently serve as a basis for an RV strategy to produce new potential vaccines against eukaryotic pathogens. We also highlight an emerging approach-structure-based vaccinology-that exploits the information derived from the determined three-dimensional structures of vaccine candidates. Regardless, genome-based RV and other vaccine discovery platforms still depend on empirical experimental science to glean, from the hundreds of identified antigens from any one pathogen, those that should be combined to produce an effective vaccine.