Demands for improved access to innovative therapies have prompted a discourse that claims patients have rights to access treatments that may be of benefit, even if evidence that demonstrates safety and efficacy is lacking. This rights-based discourse is grounded in accounts of autonomy and assertions claiming that the state ought to not interfere with the free choices of patients and clinical decision-making. In this essay, we scrutinise these arguments to defend the ethical and legal permissibility of interference in contexts where the uncertainty of benefit and potential for harm creates vulnerabilities that undermine patient capacity for self-determination. In support of this argument, we draw on two theoretical approaches to explore the limits of autonomy in innovative contexts and analyse the legal bases of the rights-based discourse. We then apply this analysis to the case example of stem cell transplantation as an innovative treatment for multiple sclerosis.