This article examines legislative changes related to abortion regulation in Australia that create obligations of medical referral on practitioners who have a conscientious objection to abortion. Despite a significant Australian history of accepting secularized conscience claims, particularly in the field of military conscription, the limitation of conscience claims about abortion can be traced to a failure to appreciate the significant secular arguments that can be made to support such claims. We draw on arguments of plurality and pragmatism as capable of providing a firm foundation for legislative protections of freedom of conscience in the case of medical referral for abortion. These justifications are not dependent on religious grounds, and therefore they have the potential to be relevant and persuasive in a secular society such as Australia. Acceptance of a pluralistic argument in favor of freedom of conscience is a powerful commitment to the creation of a society that values human autonomy and a diversity of opinion. It sits comfortably with the democratic values that are enshrined in the Australian political system and institutions. It avoids the potential damage to the individual that may be wrought when conscience is overridden by state compulsion.