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In the Region of Madrid, universal immunization with the 13-serotypes pneumococcal conjugate vaccine (PCV13) started in May 2010. In July 2012, public funding ceased. Vaccination coverage decreased from >95% to 82% in 2013 and to 67% in 2014. Our aim was to investigate the impact of PCV13 withdrawal from Madrid Region universal immunization program on the incidence of complicated pneumococcal bacteremia.We performed a multicenter retrospective cohort study, from 2009 to 2014. Participants were children aged <14 years with Streptococcus pneumoniae bacteremia. Complications were defined as any condition requiring intensive care or surgery. Sequelae were conditions lasting ≥90 days.A total of 168 patients were recruited. One-fourth of both immunized and nonimmunized patients had complications. Global complications increased after PCV13 withdrawal. About 28% of PCV13 serotypes presented complications. Complications caused by PCV13 serotypes did not increase after July 2012. Non-PCV13 serotypes increased progressively from 2009 on, and 23% presented complications. A significant risk of complications was found for patients with meningitis, empyema, C-reactive protein >100 mg/L and serotype 1. A multivariate analysis indicated that complications were associated with meningitis and hospital admission after July 2012. Sequelae were significantly associated with children <2 years of age, meningitis and non-PCV13 serotypes.The incidence of complications caused by PCV13 serotypes did not increase 2 years after PCV13 withdrawal. Nevertheless, all-serotypes complications increased. The likely cause was that non-PCV13 serotypes (associated with meningitis) are on the rise.