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Background: Measuring the quality of provided healthcare presents many challenges, especially in the context of medical rehabilitation. Rehabilitation is based on a holistic biopsychosocial model of health that includes a person's long-term functioning; hence, outcome domains are very diverse. In Germany, rehabilitation outcomes are currently assessed via patient and physician surveys. Health insurance claims data has the potential to simplify current quality assurance procedures in Germany, since its comprehensive collection is federally mandated from every healthcare provider. By using a cross-sectoral approach, quality assessments in rehabilitation can be adjusted for the quality provided in previous sectors and individual patient risk factors., Methods: SEQUAR combines two studies: In a prospective longitudinal study, 600 orthopedic rehabilitation patients and their physicians are surveyed at 4 and 2 time points, respectively, throughout rehabilitation and a follow-up period of 6 months. The questionnaires include validated instruments used in the current best-practice quality assurance procedures. In a retrospective cohort study, a nationwide claims database with more than 312,000 orthopedic rehabilitation patients will be used to perform exploratory analysis for the identification of quality indicators. The identified SEQUAR claims data quality indicators will be calculated for our prospective study participants and tested for their ability to approximate or replace the currently used, best-practice quality indicators based on primary data., Discussion: The identified SEQUAR quality indicators will be used to draft a novel, state-of-the-art quality assurance procedure that reduces the administrative burden of current procedures. Further research into the applicability to other indications of rehabilitation is required., Trial Registration: WHO UTN: U1111-1276-7141; DRKS-ID: DRKS00028747 (Date of Registration in DRKS: 2022/08/10)., (© 2023. BioMed Central Ltd., part of Springer Nature.)