This, the third annual immunisation coverage report, documents trends during 2009 for a range of standard measures derived from Australian Childhood Immunisation Register data, including overall coverage at standard age milestones and for individual vaccines included on the National Immunisation Program (NIP). Coverage by Indigenous status and mapping by smaller geographic areas as well as trends in timeliness is also summarised according to standard templates. With respect to overall coverage, the Immunise Australia Program targets have been reached for children at 12 and 24 months of age but not for children at 5 years of age. Coverage at 24 months of age exceeds that at 12 months of age, but as receipt of varicella vaccine at 18 months is excluded from calculations of 'fully immunised' this probably represents delayed immunisation, with some contribution from immunisation incentives. Similarly, the decrease in coverage estimates for immunisations due at 4 years of age from March 2008 is primarily due to changing the assessment age from 6 years to 5 years of age from December 2007. With respect to individual vaccines, a number of those available on the NIP are not currently assessed for 'fully immunised' status or for eligibility for incentive payments. These include pneumococcal conjugate and meningococcal C conjugate vaccines, for which coverage is comparable with vaccines that are assessed for 'fully immunised' status, and rotavirus and varicella vaccines for which coverage is lower. Coverage is also suboptimal for vaccines recommended for Indigenous children only (i.e. hepatitis A and pneumococcal polysaccharide vaccine) as previously reported for other vaccines for both children and adults. Delayed receipt of vaccines is an important issue for vaccines recommended for Indigenous children and has not improved among non-Indigenous children despite improvements in coverage at the 24-month milestone. Although Indigenous children in Australia have coverage levels that are similar to non-Indigenous children at 24 months of age, the disparity in delayed vaccination between Indigenous and non-Indigenous children remains a challenge.