The aim of this study was to validate geometric accuracy and in vivo reproducibility of landmark-based cephalometric measurements using high-resolution 3D Magnetic Resonance Imaging (MRI) at 3 Tesla. For accuracy validation, 96 angular and 96 linear measurements were taken on a phantom in 3 different positions. In vivo MRI scans were performed on 3 volunteers in five head positions. For each in vivo scan, 27 landmarks were determined from which 19 angles and 26 distances were calculated. Statistical analysis was performed using Bland-Altman analysis, the two one-sided tests procedure and repeated measures one-way analysis of variance. In comparison to ground truth, all MRI-based phantom measurements showed statistical equivalence (p < 0.001) and an excellent agreement in Bland-Altman analysis (bias ranges: -0.090-0.044°, -0.220-0.241 mm). In vivo cephalometric analysis was highly reproducible among the five different head positions in all study participants, without statistical differences for all angles and distances (p > 0.05). Ranges between maximum and minimum in vivo values were consistently smaller than 2° and 2 mm, respectively (average ranges: 0.88°/0.87 mm). In conclusion, this study demonstrates that accurate and reproducible 3D cephalometric analysis can be performed without exposure to ionizing radiation using MRI.