This article will explore the role of conscience in cases which are not subject to a predictable, generalisable rule-based conscientious objection. These claims arise in cases where doctors, who might have previously provided the treatment at issue, determine that the specific facts of a case mean that they cannot morally provide treatment. In legal cases, the courts have tended to act as if these conscience refusals are part of the best interests analysis. They claim that the treatment, as requested, simply is not in the best interests of the patient. However, the courts have used this analysis even when it appears clear that the refusal of treatment is not in what the patient thinks is his or her best interests. Indeed, in recent cases such as Aintree v James, the court has made it clear that determining what is in the best interests of patients usually relies more on the advice of healthcare professionals than it does on the patient's views. It is not, then, about what patients think they need or want, but what doctors and other medical staff think they can morally provide under the circumstances. This article will explore how re-conceptualising these sorts of claims as ones about conscience provides a more stable footing for understanding the legal and ethical issues which are of importance to the courts and what this might mean for these sorts of decisions in the future.