Recent reports in Australia have suggested that some medical practitioners are refusing to treat children who have not been vaccinated, a practice that has been observed in the USA and parts of Europe for some years. This behaviour, if it is indeed occurring in Australia, has not been supported by the Australian Medical Association, although there is broad support for medical practitioners in general having the right to conscientious objection. This paper examines the ethical underpinnings of conscientious objection and whether (...) the right to conscientious objection can be applied to the refusal to treat unvaccinated children. The implications of such a decision will also be discussed, to assess whether refusal to treat unvaccinated children is ethically justifiable. The best interests of both existing and new patients are crucially important in a doctor’s practice, and the tension between these two groups of patients are contemplated in the arguments below. It is argued that on balance, the refusal to treat unvaccinated children constitutes unjustified discrimination. (shrink)