Routinely collected health data (or real-world data) from hospitals is becoming increasingly important to advance medical progress. Anonymisation of these data facilitates data sharing processes. This allows stakeholders of the healthcare system to compliantly access this anonymised data to address epidemiological questions, advance precision medicine, support drug development or address other medical needs. As the willingness of the general Swiss population to share anonymised health data has been uncertain, a survey was conducted to better understand their perception of sharing such data for research purposes. The present survey focused on the re-use (secondary use) of hospital-derived health data in anonymised form. A cross-sectional survey was conducted in a representative random sample (n = 1006) of the general Swiss population. The general population was contacted by phone between 14 September and 3 October 2020. The survey was also conducted in an additional population with chronic disease (n = 225) via an online panel. An independent research organisation (gfs-zürich) was commissioned to conduct the survey. The survey participation was anonymous and voluntary. The demographic composition of the interviewed participants from the general population was specifically constructed to be representative of the 18+-year-old French- and German-speaking population of Switzerland, according to the quota features gender, age and language region. Representativeness of the chronic disease population is unclear. 71% of the general population and 81% of the chronic disease group reported that they would share their anonymised health data for medical research. The drivers were mainly of an altruistic nature. Hurdles concern mainly data protection issues, potential misuse or disadvantages, e.g., by health insurers. About 56% of the general population would like to be better informed about the use of their personal health data, and 69% spontaneously reported health authorities as the stakeholder responsible for providing such information. The survey showed that the Swiss population is willing to share anonymised health data given that some key concerns are addressed. Our findings underline that a better understanding of the standards and processes around health data privacy and transparent data usage is important to build trust in the public eye. An open dialogue is required to develop a common consent on data governance for Switzerland, which would allow health data sharing with third parties. This open dialogue should involve all stakeholders of the healthcare system, so as to strive towards both a more personalised and a more sustainable Swiss healthcare system.