Monitoring the health status of patients has become a major activity in rehabilitation research in recent years. As a result, various self-assessment instruments have been developed, adapted or improved with the aim of measuring patient-reported outcomes and predictors. Among these are international instruments, such as the NHP or the SF-36, as well as those developed in Germany, such as the IRES, the FREM-17 or the SPE-scale. Some of the widely used international instruments, such as the NHP and SF-36, have been translated into German for application in Germany. All of these instruments have been thoroughly tested and validated in several studies. Current trends in statistical methods (e.g. responsiveness, Rasch scaling) as well as classical test-theoretical standards were taken into consideration in the development of these instruments. In this article, we provide a comprehensive review of five important assessment fields of rehabilitation research in Germany: health-related quality of life (generic, disease-specific, children and adolescents, preference-based), evaluation of specific therapy and education programs, motivation, screening for vocational problems and screening for comorbid disorders. The questionnaires are critically discussed, and perspectives for further research are specified. Although assessment instruments as the IRES or the SF-36 are well-established in rehabilitation research studies, there is still a need for further research to determine the best choice of instruments for a given purpose. The limitations of the questionnaires with respect to health care studies are also discussed.