In reviewing national health systems assessments (HSAs), we identify four primary rationales for doing HSAs: (i) to motivate health systems reform, (ii) to promote harmonization and alignment across actors in the health system, (iii) to help translate health systems reforms into meaningful ways to track performance, and (iv) to facilitate learning through cross-country comparisons. We propose a set of principles to guide HSAs. These include that the HSA should be relevant, addressing the purpose for which it was designed; trustworthy in terms of being of high quality, rigorous and credible in the eyes of stakeholders; and coherent, considering the health system as a meaningful whole with linkages across system components. Given diverse rationales for undertaking HSAs, there is no one standardized framework to guide them. Frameworks and tools should be selected to reflect proposed use, and careful thought should be given to stakeholder engagement and developing local capacity for HSAs.