Many bacterial pathogens contain phase-variable methyltransferases, that control expression of multiple genes. These phase-variable regulons – phasevarions – regulate genes involved in pathogenesis, host-adaptation, and many lead to alteration of antibiotic resistance. Many phasevarions also differentially regulate putative and current vaccine candidates. For vaccines to be effective, they require that their targets are stably expressed. Individual phase-variable genes are able to be identified in silico as they contain easily recognised features. Phasevarions complicate the rational design of vaccines as the genes they regulate do not contain any identifiable features. We have studied a number of systems present in a variety of pathogens using a number of approaches: PacBio SMRT sequencing and methylome analysis deciphers the methyltransferase specificity of these systems; phenotypic analysis demonstrates global gene expression differences commensurate with methyltransferase switching; a variety of in vivo models shows host niche selection. Analysis of a large collection of nontypeable Haemophilus influenzae isolates taken from chronic obstructive pulmonary disease (COPD) patients shows a different distribution of modA alleles to that seen in children suffering from middle ear infection. Phenotypic analysis of two new modA alleles – modA15 and modA18 – show that methyltransferase switching leads to protein expression changes. Analysis of the restriction enzyme database REBASE revealed that almost one-fifth of all type III methyltransferases contain simple sequence repeats, leading to phase-variable expression, and thereby potentially controlling phasevarions. A survey of bacterial genomes for type I restriction loci reveals a number of important veterinary pathogens contain phasevarions controlled by type I methyltransferases, exemplified by the SpnD39III locus found in S. pneumoniae. Our analysis shows that phasevarions are much more widespread than previously thought, and identifies the stably expressed protein repertoire of these bacteria. This provides a framework for the rational design of vaccines and treatments against bacterial pathogens containing phasevarions.