The idea that religious institutions should play a central role in understanding the First Amendment has become increasingly prominent in recent years. Litigation over the application of civil rights laws to ministers and the requirement that religious employers provide contraception coverage to their employees have elicited calls for a doctrine of church sovereignty based on an institutional conception of the Religion Clauses. In this Article, we present grounds for skepticism about this new religious institutionalism, especially the concept of “freedom of the church,” which we distinguish from the seemingly related but importantly distinct idea of church autonomy. We further explain why individual rights of conscience are sufficient to protect the free exercise and anti-establishment values of the First Amendment. Our argument, contrary to some recent scholarship, is that religious institutions do not give rise to a special set of rights, autonomy, or sovereignty, and that what might be called institutional or church autonomy is ultimately derived from individual rights of conscience. Indeed, for purposes of understanding religious liberty, we contend that any notion of institutional autonomy — to the extent it exists — can come from nowhere else.