In order to fully appreciate the reasons behind Locke’s exclusion of atheists from toleration, it is necessary to examine his consideration of atheism against the backdrop of his theistic conception of life and morality. This chapter shows that Locke’s rejection of atheism as irrational, immoral, and thus intolerable resulted from his moral and theological commitments to natural duties stemming from the God-given Law of Nature, which he posited at the basis of the normative natural order regulating human interactions. In doing so, the chapter explains how Locke’s empiricism and anti-innatism enabled him to raise the conceptual problem of speculative atheism, in a time when only practical atheism was deemed possible because the idea of God was largely regarded as innate and, consequently, a genuine denial of God’s existence was commonly considered impossible. Nevertheless, Locke’s position concerning the legal and social measures to take against atheists is still vague and undefined.