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Key signaling pathways have been identified, but how they balance cell type composition remains unclear. We uncovered oscillatory expression of the Notch-target protein Hes1 (hairy and enhancer of split 1) that controls cell fate specification in a frequency-dependent manner. An endogenous fluorescent Hes1 reporter revealed distinct, cell type\u2013specific oscillation frequencies forming a gradient along the crypt-villus axis, which was modulated by cell cycle phase as well as Wnt (wingless-related integration site)\u2013signaling and Notch-signaling activity. We developed a microfluidic system to modulate Notch-signaling oscillations in organoids and found the oscillation frequency to regulate the balance of cell type composition. 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