Abstract Background Systemic Inflammatory Response Syndrome (SIRS) is a rare disease often presenting emergency. While the aetiology varies, current diagnostic criteria do not allow differentiation. Hopes are placed on OMICs research and development of Artificial intelligence (AI) algorithms for personalised disease management. Our report aims at identification and analysis of AI-driven ethical issues within the bigger ERA PerMed funded project of development of tailored immunotherapy for paediatric SIRS patients (TIPS) coordinated by Prof. Catharina Schütz from Technic University Dresden. Methods Systematic literature review followed by qualitative research methodology. Ten experts with different backgrounds were interviewed. Subsequent thematic analysis was performed by two independent researchers. Results Experts were on the opinion that AI can lead to a depart from individual approach in the medicine, as the physician may be induced to only act based on algorithms that are more or less representative (N = 2). Interviewees were aware that AI can lead to changes in the assessment of reality, as it is dependent on data quality (N = 4). AI-aided decision-making might be useful for special therapeutic situations, although it may not always capture the subtleties of individual situations (N = 2). Positive implications of AI were significantly more emphasised, though current frameworks were perceived as more limiting than enabling. Conclusions Personalised therapy is making its first steps while the ethical apprehensions has already been there with a strong emphasis on precautionary principle and resulting limitations on the application of AI-algorithms. The multifaceted nature of the AI-driven ethical issues in personalised medicine research requires an interdisciplinary discourse, strengthened ethics training of all professionals involved in the technology development and more active involvement of physicians in the shaping of AI. Key messages • AI algorithms promise therapeutic benefits, not achievable by other means, for specific categories of vulnerable pediatrics patients. • The multifaceted nature of the AI-driven ethical issues in personalised medicine research requires an interdisciplinary discourse and further ethics training of all stakeholders.