BACKGROUND: Finnish studies have shown a significant impact of 10-valent pneumococcal conjugate vaccine (PCV10) on nonnotified clinically suspected invasive pneumococcal disease (IPD). We used a similar vaccine probe design to estimate PCV7 and PCV13 impact in Australian children. METHODS: Season and age-matched pre-PCV7 cohorts (born in 2002-2004) were compared with PCV7-early and PCV7-late, and PCV13-eligible cohorts. Using linked notification and hospitalization data, we calculated relative rate reductions (RRRs) and absolute rate reductions (ARRs) for notified IPD, and nonnotified clinically suspected IPD or unspecified sepsis (first hospitalization with an International Classification of Diseases 10th Revision-Australian Modification code: A40.3/G00.1/M00.1 or A40.9/A41.9/A49.9/G00/I30.1/M00, respectively). RESULTS: Significant reductions in all outcomes were observed comparing PCV7-early and PCV7-late and PCV13-eligible to pre-PCV7 cohorts. RRRs were high for both notified and nonnotified clinically suspected IPD (range 71%-91%), but ARRs were lower for nonnotified (5-6/100,000 person-years) than for notified cases (59-70/100,000 person-years). RRRs for the combined outcome of nonnotified clinically suspected IPD or unspecified sepsis were lower at 21%-24% for PCV7-eligible cohorts and 36% for the PCV13-eligible cohort, but ARRs were considerable due to the high pre-PCV7 rates (ARR 37-31/100,000 person-years for PCV7-early and PCV7-late cohorts and 54/100,000 person-years for PCV13). CONCLUSIONS: This study provides a quantitative estimate of the total burden of IPD preventable by PCV7 and PCV13 vaccination programs in Australia. ARRs (compared with prevaccination) were significant but smaller than in Finland (122/100,000 for the combined outcome) and longer-term follow-up is required to determine the additional impact of PCV13 above that seen for PCV7. Country-specific studies are needed to accurately estimate the burden of pneumococcal disease preventable by vaccination and cost-effectiveness of PCV vaccination programs.