Objective: Concerns related to radiation exposure associated with three-dimensional (3D) imaging techniques of the dentomaxillofacial area have recently increased because exposure to ionizing radiation is known to be harmful. Cone-beam computed tomography (CBCT) for humans and micro-CT (µCT) for animals are the current 3D imaging standard to visualize the craniofacial skeleton. This study assessed the use of a non-ionizing imaging technique, known as SWIFT (Sweep Imaging with Fourier Transform) MRI, for the 3D analysis of human and mice craniofacial skeletons. Method: Reference standard craniofacial images of one adult human using CBCT system (8.9 seconds exposure time; FOV: 23cm x 17cm) and eight E18.5 mouse heads (two Wnt5a-/-, two Ror2-/-, four wild-type) using µCT (90kV, current: 91µA; 2000 projections) were compared to SWIFT MRI obtained using a 4T large-bore magnet and a 9.4T small-bore magnet, respectively. Qualitative assessment of 3D bone morphology and cephalometric landmark identification and linear measurements were performed on all images using available software. Result: Scan time for CBCT was 8.9 seconds (nominal resolution of 0.3mm3) and µCT was 50 minutes (nominal resolution of 0.008mm3). In comparison, scan time for SWIFT MRI of mice and human was 6.5 minutes (nominal resolution 0.078mm3). Cephalometric landmark identification presented similar technical difficulty in all four imaging datasets. Linear measurements in the SWIFT MRI were similar to those obtained using standard images techniques. Conclusion: SWIFT MRI may be an alternative method for obtaining 3D images of skeletal craniofacial structures. Implementation of this technique would reduce the radiation exposure related to craniofacial imaging applications.