This article explores the normative basis of church-state separation and of some separationist principles that apply to the conduct of individual citizens. It states institutional principles for the guidance of governmental policy toward religious institutions; it articulates citizenship standards for political conduct on the part of individuals; and it explores the case for affirming these two kinds of standards on the basis of what, historically, has been called natural reason. A major question for the article is whether natural reason may be properly considered to be secular, in a sense that implies normative authority that is not dependent on religion or theology and is also sufficient to justify affirming natural rights, such as rights to freedom of action, religious liberty, and equal treatment under the law. The article argues that natural reason may be viewed as secular in this sense and that, as has not been generally noticed, this poses a challenge to liberal political theory. On the plausible assumption that democracies may not properly assume that natural reason cannot—independently of religious premises—establish theism, they lack an adequate basis for a robust separation of church and state and cannot justify the far-reaching governmental neutrality toward religion endorsed by liberal political theory. The article assesses this challenge to liberal political theory, sketches a kind of governmental neutrality consistent with a strong conception of natural reason, and proposes a principle of toleration that supports both a desirable balance between an appropriate secularity in government and a high degree of religious liberty in society.