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Background Close, continuous and efficient collaboration between different professions and sectors of care is necessary to provide patient-centered care for individuals with mental disorders. The lack of structured collaboration between in- and outpatient care constitutes a limitation of the German health care system. Since 2012, a new law in Germany (§64b Social code book (SGB) V) has enabled the establishment of cross-sectoral and patient-centered treatment models in psychiatry. Such model projects follow a capitation budget, i.e. a total per patient budget of inpatient and outpatient care in psychiatric clinics. Providers are able to choose the treatment form and adapt the treatment to the needs of the patients. The present study (EVA64) will investigate the effectiveness, costs and efficiency of almost all model projects established in Germany between 2013 and 2016. Methods/design A health insurance data-based controlled cohort study is used. Data from up to 89 statutory health insurance (SHI) funds, i.e. 79% of all SHI funds in Germany (May 2017), on inpatient and outpatient care, pharmaceutical and non-pharmaceutical treatments and sick leave for a period of 7 years will be analyzed. All patients insured by any of the participating SHI funds and treated in one of the model hospitals for any of 16 pre-defined mental disorders will be compared with patients in routine care. Sick leave (primary outcome), utilization of inpatient care (primary outcome), utilization of outpatient care, continuity of contacts in (psychiatric) care, physician and hospital hopping, re-admission rate, comorbidity, mortality, disease progression, and guideline adherence will be analyzed. Cost and effectivity of model and routine care will be estimated using cost-effectiveness analyses. Up to 10 control hospitals for each of the 18 model hospitals will be selected according to a pre-defined algorithm. Discussion The evaluation of complex interventions is an important main task of health services research and constitutes the basis of evidence-guided advancement in health care. The study will yield important new evidence to guide the future provision of routine care for mentally ill patients in Germany and possibly beyond. Trial registration This study was registered in the database “Health Services Research Germany” (trial number: VVfD_EVA64_15_003713).