As cone-beam computed tomography (CBCT) scans become increasingly common, it is vital to have reliable 3-dimensional (3D) landmarks for quantitative analysis of craniofacial skeletal morphology. While some studies have developed and used 3D landmarks, these landmark sets are generally small and derived primarily from previous 2-dimensional (2D) cephalometric landmarks. These derived landmarks lack information in parts of the skull such as the cranial base, which is an important feature for cranial growth and development. The authors see a real need for development and validation of 3D landmarks, particularly bilateral landmarks, across the skull for improved cephalometric analysis. The primary objective of this study is to develop and validate a set of 61 3D anatomical landmarks on the face, cranial base, mandible, and teeth for use in clinical and research studies involving CBCT imaging. Each landmark was placed 3 times by 3 separate trained observers on a set of 10 anonymized CBCT patient scans. Intra-rater and inter-rater estimates of consistency and agreement were calculated using the intraclass correlation coefficient. Measurement error was calculated per landmark and per X, Y, and Z landmark coordinate. The authors had high ICC estimates within rates, indicating high consistency, and high ICC estimates among raters, indicate good agreement across raters. Overall measurement error for each landmark and each X, Y, and Z coordinate was low. Our results confirm the accuracy of novel 3D landmarks including several on the cranial base that will serve researchers and clinicians for use in future studies involving 3D CBCT imaging and craniofacial development.