Background: Some children are prone to recurrent invasive pneumococcal disease (rIPD) and of these, some respond insufficiently to standard pneumococcal vaccination. Little is known about how to handle these children and if they benefit from additional vaccination. Here, we present results from a nationwide study of pediatric rIPD including data on serotype-specific vaccination response to pneumococcal polysaccharide vaccination (PPV23) and pneumococcal conjugate vaccination (PCV7/13). Methods: A retrospective, population-based study was conducted using The National Streptococcus pneumoniae Registry, which contains laboratory-confirmed data from all cases of IPD in Denmark. From January 1980-June 2013 all children aged 0-15 years with rIPD were identified. Clinical data and data on serotype-specific pneumococcal antibody response were collected. Over the years quantification of pneumococcal antibodies varied from being presented in arbitrary units (ELISA), in μg/ml (WHO ELISA) and lately in μg/ml based on Luminex technology. Results: 2482 children were diagnosed with IPD and 75 episodes of rIPD were documented in 59 children. An underlying disease was documented in 45 (76%) children. Vaccination data were available for 26 children; 11 were vaccinated solely with PPV23, 8 with a combination of PPV23 + PCV7, 5 with PCV7 and 2 with PCV13. In total, nine responded to PPV23 vaccination and ten were PPV23 non-responders. Of the 15 PCV vaccinated children, two children responded subnormal to PCV7. Among PPV23 non-responders, five responded to subsequent PCV vaccination. Conclusions: In our population-based study of children with rIPD 53% of the children responded insufficiently to PPV23 vaccination. PPV23 non-responders benefitted from PCV vaccination.