The principle of autonomy governs much of modern, Western approaches to medicine and decision-making in the medical context. Individual freedom is perceived to be the trump card in ethical dilemmas. However, the discerning Christian will recognize that autonomy in bioethics must be filtered through a theological framework and ethic. If we are to understand our autonomy correctly, we must ask the question, what does it mean to be free? To answer this question we must develop a theology of freedom. In order to do this, I will briefly discuss the relationship between God’s sovereignty and human free will. Theologians have debated the relationship between sovereignty and free will for centuries. While the debate continues, I will suggest that the compatibilist view, which affirms both the sovereignty of God and the free will of humanity, offers a compelling model for approaching the principle of autonomy in bioethics. It helps us to see that a full theology of freedom must be developed within the context of community. True freedom is found particularly within one’s relationship with the sovereign God through Jesus Christ, which in turn informs us on the appropriate use of our freedom in relationship with others. While autonomy is often placed above other ethical frameworks, such as nonmaleficence, beneficence, and justice, a theology of freedom will incorporate these frameworks within the decision-making process of bioethical issues. In this theological mindset, autonomy is limited because true freedom is harmed when one makes decisions based solely on the individualistic level and ignores biblical virtues. True freedom only comes when we exercise our autonomy in relationship to God and fellow human beings.