Abstract Background Complementary and alternative medicine (CAM) is a rather novel issue within public healthcare and health policy-making. CAM use in Europe is widespread, patient-initiated, and patient-evaluated, and the regulation across countries has been evaluated as disharmonized. CAM users are left in an uncertain position, and patient safety may be threatened. How “risk” is understood by individuals in health policy-making and clinical encounters involving the use of CAM has not yet been much debated. The aim of this article is to explore and discuss the existence and possible consequences of differing risk understandings among stakeholders maneuvering in the complex landscape of CAM practice and CAM regulation contextualized by European public healthcare systems. Methods Qualitative data were derived from two studies on CAM in European healthcare contexts. Findings from the EU project CAMbrella on legislation and regulation of CAM were mixed with data from an interview study exploring risk understandings, communication, and decision-making among Scandinavian CAM users and their doctors. In a secondary content analysis, we constructed the case Sara as a typology to demonstrate important findings with regard to risk understandings and patient safety involving European citizens’ use of CAM in differing contexts. Results By combining and comparing individual and structural perspectives on risk and CAM use, we revealed underexplored gaps in risk understandings among individuals involved in European CAM regulation and legislation, and between CAM users and their medical doctors. This may cause health risks and uncertainties associated with CAM use and regulation. It may also negatively influence doctor-CAM user communication and CAM users’ trust in and use of public healthcare. Conclusion Acknowledging implications of stakeholders’ differing risk understandings related to CAM use and regulation may positively influence patient safety in European healthcare. Definitions of the concept of risk should include the factors uncertainty and subjectivity to grasp the full picture of possible risks associated with the use of CAM. To transform the findings of this study into practical settings, we introduce sets of questions relevant to operationalize the important question “What is risk?” in health policy-making, clinical encounters and risk research involving European patients’ use of CAM.