Supreme audit institutions (SAIs) have started to audit the implementation of the Sustainable Development Goals (SDGs). While there is no one single audit model or approach to audit SDG implementation, audits should incorporate a few core methodological features related to the principles of the 2030 Agenda. Four methodological and practical challenges associated with conducting performance audits of SDG implementation, as they differ from traditional audits, are discussed in this paper: 1) problem definition, including the level of investigation in the SDG hierarchy of goals and targets and the audit scope; 2) conceptual challenges inherent in going from the level of individual entities or programs to that of whole-of-government performance; 3) practical considerations that should inform an analysis of the coherence of government actions in a given policy area; and 4) the ways in which audit guidance at the international level can help individual SAIs going forward. Ultimately, this paper aims to inform the broader discussion on evaluation of the SDGs. 1. Introduction -- 2. Supreme audit institutions and SDG audits: A short background -- 3. Defining audits of SDG implementation -- 4. SDG audits: Exploring some implications of the definition for SAIs’ work -- 5. Understanding the subject matter of the audit: An example of generic map at the SDG target level -- 6. Where do SDG audits fit in the universe of SDG evaluation? -- 7. Conclusion.