Micro-computed tomography (micro-CT) has emerged as a transformative imaging technology in dentistry and biomedical research, offering non-invasive, high-resolution, three-dimensional visualization of dental and bone structures. This chapter explores the fundamental principles of micro-CT, its diverse applications in dentistry (including endodontics, restorative dentistry, implantology, orthodontics, and periodontology), and its role in bone tissue analysis, biomaterials research, and cancer metastasis evaluation. The integration of artificial intelligence (AI) and machine learning with micro-CT data enhances automated segmentation, tissue classification, and predictive analysis, while multimodality approaches combining micro-CT with techniques like optical coherence tomography (OCT) and magnetic resonance imaging (MRI) provide comprehensive structural and functional insights. Despite limitations such as beam hardening artifacts and small sample size requirements, advancements in nano-CT and low-dose systems are expanding the clinical potential of micro-CT. Future directions include the development of standardized protocols, real-time 3D imaging during surgical procedures, and the integration of micro-CT into clinical decision-making, paving the way for personalized and precise dental and medical treatments.