Accurate orthodontic analysis and diagnosis based on anatomical landmarks is essential to the success of orthodontic treatment. Helical computed tomography (CT) has evolved markedly, and dentists can now quickly obtain 3-dimensional (3D) reconstruction data using this imaging modality. The planning of orthodontic treatment had traditionally been based on cephalometric analysis using 2D landmarks. This study aimed to collect 3D morphological data using CT images to establish new landmarks for analysis and diagnosis in orthodontic treatment. Twenty male and 20 female adult Japanese dry skulls with of normal occlusion were selected. The skulls were scanned using a multidetector helical CT system (SIEMENS, Volume Zoom Plus 4, Germany). Models were reconstructed using 3D measurement software (Simplant, Dentsply Sirona, Tokyo, Japan) and 45 landmarks determined. Three-dimensional measurement for a total of 30 items representing these landmarks was then performed. The results provided 3D standard values for maxillofacial morphology in adult Japanese individuals with normal occlusion. These measurement items should allow the disadvantages of 2D cephalometric analysis to be overcome.