In clinical research – whether pharmaceutical, genetic or biomarker research – it is important to protect research participants’ autonomy and to ensure or strengthen their control over health-related decisions. Empirical–ethical studies have argued that both the ethical concept and the current legalistic practice of informed consent should be adapted to the complexity of the clinical environment. For this, a better understanding of recruitment, for which also the physician–patient relationship plays an important role, is needed. Our aim is to ethically reflect (...) communication processes by identifying patterns used by physicians to motivate patients’ participation in clinical research and to assess whether patients also use these patterns in formulating their own research motivation. We conducted a secondary analysis with empirical data from a research project involving physicians and patients in a clinical research setting of a biomarker study for rectal cancer treatment. Our empirical data included observations of physician–patient consultations and semi-structured interviews with patients. Overall, we collected 93 interviews. We found two dominant communication patterns, which physicians applied for motivating patients to take part in this research study. Some forms of these patterns tend to mislead patients’ understanding, while others could justifiably be applied in this consultation setting without undermining patients’ autonomy. This insight that the physician–patient communication has a strong influence on patients increases the importance to strengthen physicians’ ethically acceptable communication patterns regarding research participation. We further suggest that there is a need for a critical reflection of the ethics committee’s requirements for information regarding research participation. (shrink)