Colony stimulating factor 1 receptor (CSF1R) binds its cognate ligand, CSF1, to regulate the survival, proliferation, and differentiation of mononuclear phagocytic cells (e.g. macrophages and monocytes) and osteoclasts, the bone-resorbing cells. Studies on CSF1 and CSF1R have mainly focused on their roles in tissue-resident macrophage homeostasis, immunology, and bone biology. Here we highlight the role of CSF1R in odontogenesis (tooth development) using the mouse model. Odontogenesis occurs via epithelial and mesenchymal interactions controlled by molecular regulatory networks, ultimately resulting in the formation of specialized mineralized tissues by highly differentiated cells. During prenatal stages, mammalian teeth begin development and undergo morphogenesis, cytodifferentiation, and matrix secretion resulting in precise tooth crown shapes and early formation of enamel, dentin, and dental pulp. The formation of cementum and root elongation then follow during early postnatal stages. At later postnatal stages alveolar bone is resorbed by osteoclasts to allow teeth to erupt into the oral cavity and acquire final functions and forms. Mice completely deficient in CSF1 (Csf1op/op) or CSF1R (Csf1r-/-) fail to erupt teeth as a result of defective osteoclast formation. However, dental abnormalities associated with tooth eruption failure have also been observed in these mice postnatally. The overall objective of this study was to explain the role of CSF1R in early odontogenesis and to determine whether CSF1R has a more direct role in odontogenesis independent of that in osteoclast-mediated tooth eruption. We hypothesized that CSF1R regulates morphogenesis, cytodifferentiation, and matrix secretion during early odontogenesis. Using immunohistochemistry, we first showed the localization of CSF1R and CSF1 to be in mesenchymal tissues directly around developing teeth at early time points, and not within differentiated ameloblasts and odontoblasts. To study the impacts on developing teeth, we treated pregnant dams with the CSF1R inhibitor PLX5622 between embryonic day 3.5 (E3.5) and E18. CSF1R inhibition in mice in utero resulted in significant tooth abnormalities observed at postnatal day 21 (P21) and P28, assessed histologically and with high-resolution micro-computed tomography imaging. Importantly, irregular dental tissue infoldings and altered remodeling of bone around developing teeth were observed at prenatal time points. Notably, CSF1R inhibition in P28 mice did not impact enamel and dentin formation in the continuously growing incisors, suggesting that CSF1R does not impact dental stem cells. Together these results indicate that CSF1R regulates tooth morphology early during embryogenesis, by appropriately remodeling bony crypts forming around teeth. Identifying and studying such novel gene regulatory networks involved in the shaping and structuring of teeth will elucidate the wide morphological variations present in various dental anomalies, while also enabling advances in tooth bioengineering.