Invasive disease caused by the encapsulated bacteriaNeisseria meningitidis,Haemophilus influenzaeandStreptococcus pneumoniaeremains an important cause of morbidity and mortality worldwide, despite the introduction of successful conjugate polysaccharide vaccines that target disease-associated strains. In addition, resistance, or more accurately reduced susceptibility, to therapeutic antibiotics is spreading in populations of these organisms. There is therefore a continuing requirement for the surveillance of vaccine and non-vaccine antigens and antibiotic susceptibilities among isolates from invasive disease, which is only partially met by conventional methods. This need can be met with molecular and especially nucleotide sequence-based typing methods, which are fully developed in the case ofN. meningitidisand which could be more widely deployed in clinical laboratories forS. pneumoniaeandH. influenzae.