Streptococcus pneumoniae is both a common inhabitant of the human nasopharynx and a leading cause of morbidity and mortality. Characterisation of pneumococcal populations derived from asymptomatic carriage and invasive disease during the introduction of a 13-valent pneumococcal conjugate vaccine (PCV13) allows the impact of the vaccine to be assessed and may provide information with which to inform public health policies. Streptococcus pneumoniae isolated from the nasopharynx of healthy children were collected alongside isolates found in invasive pneumococcal disease (IPD) from the same geographical location over a ten year period. Carriage rates and IPD incidence rates were examined to assess the impact of PCV13 on both populations. Changes to the serotype distribution in both the carriage and the disease populations were compared and a molecular investigation was performed to ascertain similarities between the populations. Pneumococcal carriage and IPD incidence caused by PCV13 serotypes decreased following PCV13 introduction however an increase in carriage and IPD incidence caused by non-vaccine serotypes was observed. Evaluation of serotype distribution revealed that three non-vaccine serotypes had significantly higher odds of featuring in IPD; 12F, 8 and 9N. Genotypic analyses showed that while 83% of IPD isolates had the same clonal type as carriage isolates, some molecular variations within prevalent carriage isolates were not seen in the IPD population. The increase in carriage and IPD caused by non-vaccine serotypes is compromising the benefits of PCV use. Continued surveillance is required to safeguard public health.