Despite reducing disease, vaccination rarely protects against infection and many pathogens persist within vaccinated animal populations. Circulation of viral pathogens within vaccinated populations may favour the development of vaccine resistance with implications for the evolution of virus pathogenicity and the emergence of variant viruses. The high rate of mutations during replication of ribonucleic acid (RNA) viruses is conducive to the development of escape mutants. In vaccinated cattle, unusual mutations have been found in the major antigenic site of foot and mouth disease virus, which is also involved in receptor recognition. Likewise, atypical changes have been detected in the immunodominant region of bovine respiratory syncytial virus. Large deoxyribonucleic acid (DNA) viruses are able to recombine, generating new genotypes, as shown by the potential of glycoprotein E-negative vaccine strains of bovine herpesvirus-1 to recombine with wild-type strains. Marek's disease virus is often quoted as an example of vaccine-induced change in pathogenicity. The reasons for this increase in virulence have not been elucidated and possible explanations are discussed.