Since the introduction of childhood pneumococcal conjugate vaccines, invasive pneumococcal disease (IPD) incidence has decreased in children and the predominant serotypes causing disease have changed. This study describes changes in the clinical features of IPD in children (<18 years) before and after conjugate vaccine introduction.The Calgary Area Streptococcus pneumoniae Epidemiology Research (CASPER) study collects information on all IPD cases in Calgary, Alberta, Canada. Descriptive and regression analyses were used to compare IPD in the pre-vaccine (2000-August 2002), post-PCV7 (September 2002-June 2010), and post-PCV13 (July 2010-December 2015) periods; ICU and inpatient admissions were outcome measures.The incidence of IPD in children (<18 years) decreased from an average of 17 cases/100,000/year in 2000/2001 to 4 cases/100,000/year in 2015. The median age of children presenting with IPD shifted from 2.0 years (IQR:2.5) in the pre-vaccine period to 3.9 years (IQR:6.2) in the post-PCV13 period. The proportion of children with a comorbidity that is an indication for pneumococcal vaccination did not change. Invasive disease with focus (meningitis, pneumonia, empyema, peritonitis) compared with invasive disease with bacteremia only increased from 44.6% in pre-vaccine to 64.0% and 61.4% in the post-PCV7 and post-PCV13 periods respectively (P=0.017). Having IPD in the post-PCV13 period compared with the pre-vaccine period was associated with an increased odds of hospitalization (OR: 2.9; 95% CI:1.4-6.2).Clinical features of IPD have changed since pneumococcal conjugate vaccines were introduced, with a shift towards more focal infections requiring hospitalization. Although overall IPD cases have declined, disease that does occur appears to be more severe.