There are currently 370 million persons identifying as indigenous across 90 countries globally. Indigenous peoples generally face substantial exclusion/marginalization and poorer health status compared with non-indigenous majority populations; this includes poorer oral health status and reduced access to dental services. Population-level oral health surveys provide data to set priorities, inform policies, and monitor progress in dental disease experience/dental service utilisation over time. Rigorously and comprehensively measuring the oral health burden of indigenous populations is an ethical issue, though, given that survey instruments and sampling procedures are usually not sufficiently inclusive. This results in substantial underestimation or even biased estimation of dental disease rates and severity among indigenous peoples, making it difficult for policy makers to prioritise resources in this area. The methodological challenges identified include: (1) suboptimal identification of indigenous populations; (2) numerator-denominator bias and; (3) statistical analytic considerations. We suggest solutions that can be implemented to strengthen the visibility of indigenous peoples around the world in an oral health context. These include acknowledgment of the need to engage indigenous peoples with all data-related processes, encouraging the use of indigenous identifiers in national and regional data sets, and mitigating and/or carefully assessing biases inherent in population oral health methodologies for indigenous peoples.