Methods for calculating health indicators profoundly influence understanding of and action on population health and inequities. Age-standardization can be useful and is commonly applied to account for differences in age structures when comparing health indicators across groups. Age-standardized rates have well-acknowledged limitations, including that they are relative indices for comparison, and not accurate measures of actual rates where the age structures of groups diverge. This paper explores these limitations, and demonstrates alternative approaches through a case study quantifying mortality rates within the Aboriginal and Torres Strait Islander (Indigenous) population of Australia and inequities compared with the non-Indigenous population, over 2001–16. Applying the Australian Standard Population, the Aboriginal and Torres Strait Islander age-standardized mortality rate was more than double the crude mortality rate in 2001 and 2016, inflated through high weighting of older age groups. Despite divergent population age structures, age-standardized mortality rates remain a key policy metric for measuring progress in reducing Indigenous-non-Indigenous inequities in Australia. Focusing on outcomes age-standardized to the total population can obscure inequities, and denies Aboriginal and Torres Strait Islander peoples and communities valid, actionable information about their health and well-being. Age-specific statistics convey the true magnitude of health risks and highlight high-risk subgroups. When requiring standardization, standardizing to a population-specific standard (here, an Indigenous standard) generates metrics centred around and reflective of reality for the population of focus, supporting communities’ self-determination to identify priorities and informing resource allocation and service delivery. The principles outlined here apply across populations, including Indigenous and other populations internationally.