Immunoinformatics is the application of informatics techniques to molecules of the immune system. One of the key goals of immunoinformatics is the development of computer aided vaccine design (CAVD), or computational vaccinology, and its application to the search for new vaccines. Key to solving this challenge is the prediction of immunogenicity, be that at the level of epitope, subunit vaccine or attenuated pathogen. This paper reviews the current state of play in the prediction of immunogenicity and focuses on well developed methods for the prediction of peptide binding affinity to major histocompatibility complexes, which are the necessary preliminary to the in silico identification of T cell epitopes.