This paper argues that secular legal systems need a better defined space for freedom of conscience because this important right has been crowded out by both freedom of religion and freedom of thought. Based on the principles of the Protestant Reformation, American constitutionalism expanded the idea of freedom of conscience to the point of making it almost interchangeable with freedom of religion. On the other hand, international law, followed by European constitutional law, reduced the political force of the concept of freedom of conscience by assimilating it to freedom of thought. And yet freedom of conscience cannot be treated just the same as either religious freedom or freedom of thought. By nature, the secular legal systems of political communities are moral, but nonreligious. So morality and religion affect legal systems in different ways. For this reason, freedom of conscience and freedom of religion should be protected using different legal devices. The so-called privilege of abstaining (beneficium abstinendi) best protects freedom of conscience; freedom of religion, by contrast, is appropriately protected by what I call the religious exception (exceptio religiosa). The consequences of applying these legal tools in particular cases, and their proper scopes, depend on the constitutional model of the political community in question. But in general, an increasingly globalized, diverse, and multicultural society demands a wider application of both these legal tools.