OBJECTIVE: To investigate the relationship between ISO 9001 certification, healthcare accreditation and quality management in European hospitals. DESIGN: A mixed method multi-level cross-sectional design in seven countries. External teams assessed clinical services on the use of quality management systems, illustrated by four clinical pathways. SETTING AND PARTICIPANTS: Seventy-three acute care hospitals with a total of 291 services managing acute myocardial infarction (AMI), hip fracture, stroke and obstetric deliveries, in Czech Republic, France, Germany, Poland, Portugal, Spain and Turkey. MAIN OUTCOME MEASURE: Four composite measures of quality and safety [specialized expertise and responsibility (SER), evidence-based organization of pathways (EBOP), patient safety strategies (PSS) and clinical review (CR)] applied to four pathways. RESULTS: Accreditation in isolation showed benefits in AMI and stroke more than in deliveries and hip fracture; the greatest significant association was with CR in stroke. Certification in isolation showed little benefit in AMI but had more positive association with the other conditions; greatest significant association was in PSS with stroke. The combination of accreditation and certification showed least benefit in EBOP, but significant benefits in SER (AMI), in PSS (AMI, hip fracture and stroke) and in CR (AMI and stroke). CONCLUSIONS: Accreditation and certification are positively associated with clinical leadership, systems for patient safety and clinical review, but not with clinical practice. Both systems promote structures and processes, which support patient safety and clinical organization but have limited effect on the delivery of evidence-based patient care. Further analysis of DUQuE data will explore the association of certification and accreditation with clinical outcomes.