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Therapeutic misconception is a well-known challenge for informed decision-making for cancer research participants. What is still missing, is a detailed understanding of the impact of “personalised” treatment research (e.g. biomarkers for stratification) on research participants. For this, we conducted the first longitudinal empirical-ethical study based on semi-structured interviews with colorectal cancer patients (n = 40) enrolled in a biomarker trial for (neo)adjuvant treatment, analysing the patients’ understanding of and perspectives on research and treatment with qualitative methods. In addition to therapeutic misconception based on patients’ confusion of research and treatment, and here triggered by misled motivation, information paternalism or incomprehension, we identified genetic misconception and genetic responsibility as new problematic issues. Patients mainly were not aware of the major research aim of future stratification into responders and non-responders nor did they fully acknowledge this as the aim for personalised cancer research. Thus, ethical and practical reflection on informed decision-making in cancer treatment and research should take into account the complexity of lay interpretations of modern personalised medicine. Instead of very formalistic, liability-oriented informed consent procedures, we suggest a more personalised communication approach to inform and motivate patients for cancer research.