BACKGROUND: Trends in age specific and serotype specific incidence rates for invasive pneumococcal disease (IPD) were examined in South Australia 4 years before and 5 years after the commencement of the Australian universal childhood 7 valent pneumococcal conjugate vaccine (7vPCV) program. METHODS: IPD cases were identified by routine enhanced surveillance. IPD serotypes were grouped according to those covered by the 7vPCV, the six serotypes specific to the 13 valent pneumococcal conjugate vaccine (13vPCV), the 11 serotypes specific to the 23 valent pneumococcal polysaccharide vaccine (23vPPV), as well as non-13vPCV and non-23vPPV groups. Poisson regression was used to calculate age-specific and serotype-specific incident rate ratios (IRRs) comparing pre (2002-2004) and post (2007-2009) universal childhood 7vPCV periods. RESULTS: Following the introduction of the 7vPCV program, the rate of IPD in children aged <2 years decreased by 81% for all serotypes (IRR 0.19, 95% CI, 0.13-0.28) and by 98% for 7vPCV serotypes (IRR 0.02, 95% CI, 0.007-0.07). At the same time, there was some evidence for an increase in IPD caused by 13vPCV specific serotypes (IRR 1.58, 95% CI, 0.78-3.21) and non-13vPCV serotypes (IRR 1.80, 95% CI, 0.45-7.21). Among adults aged ≥65 years, overall there was a 27% reduction in IPD caused by all serotypes following introduction of the 7vPCV program (IRR 0.73, 95% CI, 0.58-0.93). However, the rate of IPD increased in the last 2 years of the study period. The initial decrease was a result of a 74% reduction in the rate of IPD due to 7vPCV serotypes (IRR 0.26, 95% CI, 0.17-0.40). At the same time, the rate of IPD increased for 13vPCV specific serotypes (IRR 1.55, 95% CI, 0.94-2.54), 23vPPV specific serotypes (IRR 1.91, 95% CI, 0.99-3.71) and particularly non-23vPPV serotypes (IRR 5.3, 95% CI, 1.83-15.34). CONCLUSION: There has been a large direct and sustained benefit from the universal 7vPCV program in children, particularly those aged <2 years, with some evidence for serotype replacement. There is also good evidence that the childhood program has provided indirect benefits to adults aged ≥65 years, although serotype replacement has reduced the initial benefits.