This study aimed to evaluate a commercial micro-CT system (μCT 20) for quantitative analysis of mineral concentration in human enamel and dentin using different methodologies, and thereby compare the obtained results with established data from published literature. A micro-CT device set at 50 kVp (160μA) was used to scan five whole molars (G1) and five molars ground to 6-mm thickness (G2) , as well as evaluate the mineral concentration of the samples. Mean mineral contents for enamel and dentin were 2.57 (±0.12) and 1.53 (±0.12) g/ cm³ for G1, and 2.76 (±0.03) and 1.45 (±0.02) g/ cm³ for G2. Difference between the groups was significant for enamel. For dentin, there was a clear although not significant tendency towards higher values with G1. The equipment could identify and differentiate a higher mineral content of the tooth enamel and dentin from the external to the inner tissue. Further, the absolute mean values of mineral concentration were lower in whole tooth samples than in sectioned samples due to beam hardening. In conclusion, the equipment is well suited for quantifying the mineral content of teeth. However, it is necessary to consider the limited acceleration voltage of the μCT 20 system and to limit sample evaluation to 6-mm thickness.