Most cells possess non-motile primary cilia that act as cellular antennas. We hypothesize that ablation of primary cilia on Sertoli cells will inhibit morphogenesis and disrupt hedgehog signaling. ODF2, a protein essential for cilia formation, and IFT88, a protein essential for ciliary transport, were targeted using CRISPR-Cas9 and siRNA techniques, respectively, to ablate cilia. Knockdown of ODF2 and IFT88 resulted in a significant reduction in the number of cells with primary cilia and significant shortening of the remaining cilia. Knockdown of both targets also disrupted formation of testicular organoids and tubules in vitro. Only reduction of IFT88 and not ODF2 resulted in attenuated hedgehog signalling. Neither this loss nor treatment with cyclopamine resulted in changes in in vitro morphology or expression of genes downstream of the hedgehog pathway. These results show that primary cilia are important for morphogenesis in vitro but hedgehog signaling is not the cilia-mediated pathway responsible.