Infectious diseases are the greatest cause of global morbidity and mortality. About half of this burden is caused by pathogenic bacteria. One of the most effective ways to prevent infectious diseases is to use vaccines. Limitations in the traditional approaches may be one of the reasons why vaccines are yet not available against some infectious bacterial agents. Recent advancements in high-throughput 'omics' technologies and the availability of complete genome sequences of microbial pathogens and multiple isolates of the same species have dramatically changed the time frame and scope for identifying novel vaccine candidates. At present, 582 microbial genomes have been sequenced and sequencing of 1733 is in progress. There are more than 50 bacterial species for which the genome sequence is available for three or more isolates. Development of tools for in silico analysis has led to the identification of novel virulence genes, metabolic pathways and cell surface proteins that represent potential new targets for anti-microbial drug and vaccine strategies. In this review, we provide an overview of the 'omics'-based techniques that can be used to advance and accelerate the discovery of vaccine candidates against extracellular bacterial pathogens. By citing specific examples, we discuss how high-throughput molecular profiling techniques, such as genomics, transcriptomics and proteomics have contributed to the discovery of novel vaccine candidates. We end by contemplating on the emerging technologies that are likely to have a high impact on the field of vaccinology in the near future.