Despite the growing body of research on quality and safety in healthcare, there is little evidence of the association between the way hospitals are organised for quality and patient factors, limiting our understanding of how to effect large-scale change. The 'Deepening our Understanding of Quality in Australia' (DUQuA) study aims to measure and examine relationships between (1) organisation and department-level quality management systems (QMS), clinician leadership and culture, and (2) clinical treatment processes, clinical outcomes and patient-reported perceptions of care within Australian hospitals. The DUQuA project is a national, multilevel, cross-sectional study with data collection at organisation (hospital), department, professional and patient levels. Sample size calculations indicate a minimum of 43 hospitals are required to adequately power the study. To allow for rejection and attrition, 70 hospitals across all Australian jurisdictions that meet the inclusion criteria will be invited to participate. Participants will consist of hospital quality management professionals; clinicians; and patients with stroke, acute myocardial infarction and hip fracture. Organisation and department-level QMS, clinician leadership and culture, patient perceptions of safety, clinical treatment processes, and patient outcomes will be assessed using validated, evidence-based or consensus-based measurement tools. Data analysis will consist of simple correlations, linear and logistic regression and multilevel modelling. Multilevel modelling methods will enable identification of the amount of variation in outcomes attributed to the hospital and department levels, and the factors contributing to this variation. Ethical approval has been obtained. Results will be disseminated to individual hospitals in de-identified national and international benchmarking reports with data-driven recommendations. This ground-breaking national study has the potential to influence decision-making on the implementation of quality and safety systems and processes in Australian and international hospitals.