BACKGROUND: Most tooth cavities start to develop inside pits and fissures where brushing, saliva, fluoride toothpaste or mouthwashes have no access. Therefore, 3D morphology of pits and fissures is an important subject to be studied in relation to maintaining proper oral hygiene. OBJECTIVE: This study aimed to present high resolution images of pits and fissures in human teeth using a laboratory-based micro X-ray Computed Tomography (mXCT) and also to present the basic structure evaluation that could be obtained. METHODS: Three human wisdom teeth were examined. Two different set-ups were used in this study achieving resolution of 14.59 μm (Field of View of 14.9 mm) and resolution of 4.43 μm (FOV of 4.5 mm) respectively. Automated segmentation was performed for further evaluation to distinguish between empty space (pits and fissures) and the filled space (enamel). RESULTS: The 3D tomography results demonstrate detailed morphology with accurate dimensions and the locations of the pits and fissures, which is important to investigate the relationship with tooth decay that mostly starts deep inside pits and fissures. CONCLUSIONS: Segmentation from the mXCT imaging of pits and fissures provides obvious visual evidence to help in promotion of oral health and to improve personal tooth care in preventive treatment protocols.