To describe an increase in the incidence of invasive pneumococcal disease (IPD) caused by serotypes not contained in the heptavalent pneumococcal conjugate vaccine (PCV7) in children in two hospitals in Barcelona with different vaccine uptake. Cumulative incidences of IPD, vaccine and nonvaccine serotypes (NVSTs), and main clinical presentations before (1998-2001) and after vaccine introduction (2005-2008) were compared. The incidence of IPD in children aged <2 years at Hospital Germans Trias i Pujol covering a population in which PCV7 was not widely used showed a nonsignificant increase from 29.9 to 58.8 per 100,000 child-years between both periods. Following vaccine introduction, there was a 2.5-fold increase in IPD caused by NVSTs in children aged <5 years. Analysis of trends in the almost fully vaccinated population of Hospital de Barcelona revealed a nonsignificant reduction in IPD incidence in children aged <2 years from 63.1 to 26.0 per 100,000 child-years. NVSTs in children aged <5 years showed a nonsignificant 1.7-fold increase in the vaccine period at this centre. The paradoxical increase in invasive infections caused by NVSTs in these populations with different vaccine use suggests that these changes were not driven only by PCV7.