Objectives: To obtain, through a survey, estimates of immunisation coverage in a birth cohort of Indigenous children, and to compare survey estimates with those obtained from the Australian Childhood Immunisation Register (ACIR) for the same birth cohort of Indigenous children.

Methods: Cluster sampling of a birth cohort of two-year-old Indigenous children across Queensland, stratified according to accessibility/remoteness from services, was undertaken in 2003. An innovative method of identifying participants was used. Survey results of 10 vaccine doses were compared with ACIR data.

Results: The survey obtained a 4% sample of the birth cohort (137 children). Universally recommended vaccines showed high levels of coverage at 12 and 24 months, and survey estimates were slightly higher than ACIR estimates. Diphtheria-tetanus-acellular pertussis vaccine dose 3 (DTPa3) coverage was 93.8% (95% CI 88.0–99.6) by 12 months on survey and 87.5% on ACIR. Coverage was not timely and a lag phase of 4–6 months occurred for each vaccine dose. Haemophilus influenzae type b vaccine dose 2 (Hib2), scheduled for the age of four months, reached 90% coverage by nine months of age in the survey children.

Conclusion: Both methods reported here provided similar results.

Implications: These data indicate that ACIR Indigenous reporting rates have increased and coverage estimates are comparable to those provided by a survey. Immunisation coverage appears to be high, and the main remaining challenge in further reducing vaccine-preventable disease in Indigenous children is to improve immunisation timeliness.