Background The recognition of serious pathologies affecting the musculoskeletal (MSK) system, especially in the early stage of a disease, is an important but challenging task. The prevalence of such serious pathologies is currently low. However, in our progressing aging population, it is anticipated that serious pathologies affecting the MSK system will be on the rise. Physiotherapists, as part of a wider health care team, can play a valuable role in the recognition of serious pathologies. It is at present unknown how accurately Austrian qualified physiotherapists can detect the presence of serious pathologies affecting the MSK system and therefore determine whether physiotherapy management is indicated (keep patients) or not (refer patients to a medical doctor). Objective We will explore the current ability of Austrian qualified physiotherapists to recognize serious pathologies by using validated clinical vignettes. Methods As part of an electronic web-based survey, these vignettes will be distributed among a convenience sample of qualified Austrian physiotherapists working in a hospital or private setting. The survey will consist of four sections: (1) demographics and general information, (2) the clinical vignettes, (3) questions concerning the clinical vignettes, and (4) self-perceived knowledge gaps and learning preferences from the perspective of study participants. Results will further be used for (1) international comparison with similar studies from the existing literature and (2) gaining insight into the participants’ self-perceived knowledge gaps and learning preferences for increasing their knowledge level about keep-refer decision-making and detecting serious pathologies. Results Data collection took place between May 2022 and June 2022. As of June 2022, a total of 479 Austrian physiotherapists completed the survey. Data analysis has started, and we aim to publish the results in 2023. Conclusions The results of this survey will provide insights into the ability of Austrian physiotherapists to make accurate keep-refer decisions and to recognize the presence of serious pathologies using clinical vignettes. The results of this survey are expected to serve as a basis for future training in this area. International Registered Report Identifier (IRRID) DERR1-10.2196/43028