Sphenoid wing dysplasia (SWD), which results in a craniofacial deformity, is the third most common skeletal deformity in Neurofibromatosis Type I (NF1) patients. A neurofibromin osteoblast conditional deletion mouse model (Nf1ob-/-) has been developed to study the skeletal abnormalities in NF1. No overt morphological phenotype is seen in the appendicular or axial skeleton of these mice. Nf1ob-/-mice have been shown to have increased bone porosity and lower bone density. We noted a progressive craniofacial deformity, which results in cranial asymmetry, malocclusion and unilateral proptosis of an eye. To assess this deformity, we employed micro-computed tomography (µCT) and geometric morphometric analysis to compare Nf1ob-/-mouse skulls to control animals. Landmarks were placed on the images at 13 biologically relevant cranial anatomical sites. Analysis of distances and angles between these landmarks revealed that there is significant variation between the Nf1ob-/-mice and controls. We found that the nasal and frontal bones of Nf1ob-/-mice skulls are deviated from the central line, whereas it was straight in controls. The nasal region is tipped downward in Nf1ob-/-mice. We also noted that the cranium shows a trend toward macrocephaly in Nf1ob-/-mice whereas other measurements were within the range of normal control mice. These differences correspond to those seen in craniofacial dysplasia and SWD in NF1 patients. No tumors were found associated with the craniofacial dysplasia in Nf1ob-/-mice. Our results identify a primarily osteoblast origin for the pathogenesis of craniofacial dysplasia in Nf1ob-/-mice and strongly support an osteoblast origin for SWD in NF1. In addition, we identify and validate a novel mouse model with which to explore molecular mechanisms and test preventative treatments for SWD in NF1.