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The very first words of the very first amendment to the United States Constitution continue to frustrate the quest for constitutional clarity. The Bill of Right’s Establishment Clause commands in plain terms that “Congress shall make no law respecting an establishment of religion,” but the legal interpretation and political implications of the Clause remain contested today as ever before. What may government require of religion? What may religion demand of government? How much of its independence must religion cede to government? And how closely may government collaborate with religion? These enduring questions admit of no definitive answers, at least not without an organizing logic that can bring coherence and purpose to the Establishment Clause. In this Article, I suggest that the concept of the separation of powers can help do just that. Using separation of powers theory, I construct a framework for clarifying the meaning of the Establishment Clause, giving political actors guidance for crafting policy pursuant to it, and making predictable its interpretation in courts.