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Background Invasive pneumococcal disease ( IPD) became a notifiable disease in New Zealand in 2008, and in the same year pneumococcal conjugate vaccine ( PCV) was added to the childhood immunisation schedule. Design This was a retrospective study of IPD in infants aged <90 days reported to the national notifiable disease database, EpiSurv, from 1 January 2009 to 31 December 2013. All cases had Streptococcus pneumoniae isolated from a normally sterile site. Main outcome measures IPD incidence was calculated for babies aged <90 and <30 days using the number of national IPD cases with a denominator of annual infant live births. Clinical, demographic and outcome data were reviewed for infants aged less than seven days (early onset). Results There were 29 cases of IPD in infants aged <90 days and 19 cases in infants aged <30 days. Of the nine early-onset cases, six occurred within the first 48 h. Six of the early-onset cases were infants of NZ Maori ethnicity. One infant died six hours after birth. Three infants developed long-term neurological or respiratory sequelae. Isolates from five of the early-onset cases were S. pneumoniae serotypes not covered by the PCV in use at the time of infection. Maternal vaccination with 23-valent pneumococcal vaccine would have covered 84% (16 of 19) of serotypes responsible for the cases in infants <30 days old. Conclusion Strategies such as maternal vaccination or accelerated neonatal vaccination may be beneficial to protect neonates at high risk of IPD. [ABSTRACT FROM AUTHOR]