Enhanced surveillance for invasive pneumococcal disease (IPD) has been ongoing in Western Australia since 1996. We describe the epidemiology of invasive pneumococcal disease in children aged <2 years between 1996 and 2005. Pneumococcal conjugate vaccine has been offered to Aboriginal children and other high-risk children since July 2001 and to all Australian children since January 2005. A total of 1655 IPD cases were reported of whom 361 (55 Aboriginal) were aged <2 years. From 1996-2001 to 2002-2005, IPD incidence declined from 192 to 124/100,000/annum in Aboriginal children and from 70 to 56/100,000/annum in non-Aboriginal children. Incidence of IPD due to vaccine serotypes (VT) declined from 118 to 43/100,000/annum (p=0.05) in Aboriginal children and from 59 to 45/100,000/annum in non-Aboriginal children (p<0.001), with no increased incidence of disease due to non-vaccine serotypes. Continued surveillance is essential to measure the impact of the childhood pneumococcal conjugate vaccination program on IPD incidence and to identify the emergence of disease due to non-vaccine serotypes.