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Endothelial-to-mesenchymal transition (EndoMT) is an instrumental step in the development of valves in the embryonic heart. This process is driven by activation of transforming growth factor–β (TGF-β) signaling and is characterized by the loss of endothelial and gain of mesenchymal phenotype, and by delamination of cells from the surface into the underlying endocardial cushion matrix. The endothelial cells (ECs) overlying the cushions are typically exposed to high blood flow and concomitant shear stress and do not have a primary cilium. Here, we show that shear stress activates TGF-β–Alk5 signaling in ECs, which is necessary for EndoMT in the cushions. Moreover, we show that the absence of a primary cilium is critically important for this transition process.