The aim of this letter to the editor is to provide a comprehensive summary of uncertainty assessment in Health Technology Assessment, with a focus on transferability to the setting of rare diseases. The authors of “TRUST4RD: tool for reducing uncertainties in the evidence generation for specialised treatments for rare diseases” presented recommendations for reducing uncertainty in rare diseases. Their article is of great importance but unfortunately suffers from a lack of references to the wider uncertainty in Health Technology Assessment and research prioritisation literature and consequently fails to provide a trusted framework for decision-making in rare diseases. In this letter to the editor we critique the authors’ tool and provide pointers as to how their proposal can be strengthened. We present references to the literature, including our own tool for uncertainty assessment (TRUST; unrelated to the authors’ research), apply TRUST to two assessments of orphan drugs in rare diseases and provide a broader perspective on uncertainty and risk management in rare diseases, including a detailed research agenda.