The study of inequities in health is a critical component of monitoring government obligations to uphold the rights of Indigenous Peoples. In Aotearoa/New Zealand the indigenous Māori population has a substantially younger age structure than the non-indigenous population making it necessary to account for age differences when comparing population health outcomes. An age-standardised rate is a summary measure of a rate that a population would have if it had a standard age structure. Changing age standards have stimulated interest in the potential impact of population standards on disparities data and consequently on health policy. This paper compares the age structure of the Māori and non-Māori populations with two standard populations commonly used in New Zealand: Segi's world and WHO world populations. The performance of these standards in Māori and non-Māori mortality data was then measured against the use of the Māori population as a standard. It was found that the choice of population standard affects the magnitude of mortality rates, rate ratios and rate differences, the relative ranking of causes of death, and the relative width of confidence intervals. This in turn will affect the monitoring of trends in health outcomes and health policy decision-making. It is concluded that the choice of age standard has political implications and the development and utilisation of an international indigenous population standard should be considered.