Background: The one of the most recent imaging technology is X-ray microtomography which allows non-invasive three-dimensional visualisation of structures. It also offers the opportunity to conduct a comprehensive quantitative analysis of the tested objects such as measuring the shares of the various phases, determining the material density and distribution of the size of pores and particles. The aim of the paper was to present an overview on the applicability and relevance of X-ray microtomography in the study of mineralised tissues of the teeth. Materials and methods: The article is based on the most recent and significant literature and own observations. Results: The use of X-ray microtomography in dentistry has recently increased and includes, inter alia, the assessment of the density of minerals in enamel and dentin, the detection of demineralisation in an artificially and a naturally induced caries, the automatic measurement of the depth of cavities in dentin, the measurement of the amount of removed dentin in preparation of carious lesions by various methods, the assessment of microleakage around fillings and fissure sealants, cortical bone density measurement, evaluation of root canal morphology, comparison of the accuracy of root canal working and filling by various methods. Conclusions: X-ray microtomography offers within the analysis of mineralised tissues — complex structures of bone, teeth and biomedical materials, turn out to be indispensable since it opens new opportunities for cognitive and implementation research. (Folia Morphol 2017; 76, 2: 143–148)