Abstract Background Verbal autopsy is a pragmatic approach for generating cause-of-death data in contexts without well-functioning civil registration and vital statistics systems. It has primarily been conducted in health and demographic surveillance systems (HDSS) in Africa and Asia. Although significant resources have been invested to develop the technical aspects of verbal autopsy, ethical issues have received little attention. We explored the benefits and burdens of verbal autopsy in HDSS settings and identified potential strategies to respond to the ethical issues identified. Methods This research was based on a case study approach centred on two contrasting HDSS in Kenya and followed the Mapping-Framing-Shaping Framework for empirical bioethics research. Data were collected through individual interviews, focus group discussions, document reviews and non-participant observations. 115 participants were involved, including 86 community members (HDSS residents and community representatives), and 29 research staff (HDSS managers, researchers, census field workers and verbal autopsy interviewers). Results The use of verbal autopsy data for research and public health was described as the most common potential benefit of verbal autopsy in HDSS. Community members mentioned the potential uses of verbal autopsy data in addressing immediate public health problems for the local population while research staff emphasized the benefits of verbal autopsy to research and the wider public. The most prominent burden associated with the verbal autopsy was emotional distress for verbal autopsy interviewers and respondents. Moral events linked to the interview, such as being unsure of the right thing to do (moral uncertainty) or knowing the right thing to do and being constrained from acting (moral constraint), emerged as key causes of emotional distress for verbal autopsy interviewers. Conclusions The collection of cause-of-death data through verbal autopsy in HDSS settings presents important ethical and emotional challenges for verbal autopsy interviewers and respondents. These challenges include emotional distress for respondents and moral distress for interviewers. This empirical ethics study provides detailed accounts of the distress caused by verbal autopsy and highlights ethical tensions between potential population benefits and risks to individuals. It includes recommendations for policy and practice to address emotional and moral distress in verbal autopsy.