We compared serotype distributions of Streptococcus pneumoniae isolates from patients aged <5 and ≥ 5 years with invasive pneumococcal disease in New South Wales, Australia, and antibiotic susceptibilities of isolates from the <5 years age group only, before (2002–2004) and after (2005–2009) introduction of the 7-valent pneumococcal conjugate vaccine (PCV7). Overall, there were significant decreases in the mean annual number of referred isolates (770 vs. 515) and the proportion belonging to PCV7 serotypes (74% vs. 38%), but non-PCV7 serotypes, particularly 19A, increased (5% vs. 18%). All changes were more marked in the <5 years age group. Susceptibility testing of isolates from the <5 years age group showed variation in resistance between serotypes, but significant overall increases in penicillin non-susceptibility (23% vs. 31%), ceftriaxone resistance (2% vs. 12%) and multidrug resistance (4% vs. 7%) rates; erythromycin resistance fell (32% vs. 25%). Continued surveillance is needed to monitor changes following the introduction of 13-valent PCV in 2012.