Cilk1 is essential for maintaining mesenchymal primary cilia and ensuring effective signaling required for intestinal villus morphogenesis. Disruption of Cilk1 impairs Hh-mediated mesenchymal clustering, with additional effects on BMP and Wnt pathways contributing to the developmental defects. These findings establish the critical role of Cilk1-dependent mesenchymal ciliogenesis in epithelial-mesenchymal communication during intestinal development.