Streptococcus pneumoniae isolates express one of more than 90 polysaccharide capsule variants (known as serotypes, which can be further classified into serogroups) that are the target of current vaccines. However, bacteria can change their serotype through recombination to evade vaccine-induced immunity. Croucher et al. assessed whether patterns in serotype switching occur by examining a collection of 616 whole-genome pneumococcal sequences that were collected following routine vaccination. They found an increased rate of within-serogroup switching than that expected by chance, which could not be fully explained by more frequent recombination, genetic epistasis or bacterial metabolism. These data provide novel insight into vaccine-induced bacterial evolution, but further studies are required to identify the determinants of within-serogroup switching.