© 2020 The Author(s). Background: The lack of attention to Indigenous epistemologies and, more broadly, Indigenous values in primary research, is mirrored in the standardised critical appraisal tools used to guide evidence-based practice and systematic reviews and meta-syntheses. These critical appraisal tools offer no guidance on how validity or contextual relevance should be assessed for Indigenous populations and cultural contexts. Failure to tailor the research questions, design, analysis, dissemination and knowledge translation to capture understandings that are specific to Indigenous peoples results in research of limited acceptability and benefit and potentially harms Indigenous peoples. A specific Aboriginal and Torres Strait Islander Quality Appraisal Tool is needed to address this gap. Method: The Aboriginal and Torres Strait Islander Quality Appraisal Tool (QAT) was developed using a modified Nominal Group and Delphi Techniques and the tool's validity, reliability, and feasibility were assessed over three stages of independent piloting. National and international research guidelines were used as points of reference. Piloting of the Aboriginal and Torres Strait Islander QAT with Aboriginal and Torres Strait Islander and non-Indigenous experts led to refinement of the tool. Results: The Aboriginal and Torres Strait Islander QAT consists of 14 questions that assess the quality of health research from an Aboriginal and Torres Strait Islander perspective. The questions encompass setting appropriate research questions; community engagement and consultation; research leadership and governance; community protocols; intellectual and cultural property rights; the collection and management of research material; Indigenous research paradigms; a strength-based approach to research; the translation of findings into policy and practice; benefits to participants and communities involved; and capacity strengthening and two-way learning. Outcomes from the assessment of the tool's validity, reliability, and feasibility were overall positive. Conclusion: This is the first tool to appraise research quality from the perspective of Indigenous peoples. Through the uptake of the Aboriginal and Torres Strait Islander QAT we hope to improve the quality and transparency of research with Aboriginal and Torres Strait Islander peoples, with the potential for greater improvements in Aboriginal and Torres Strait Islander health and wellbeing.