Nondestructive, three-dimensional (3-D) element-concentration mapping was performed and high spatial resolution and quantitative applicability were demonstrated. X-ray computed tomography using synchrotron radiation developed at SPring-8 (SP-μCT) enabled us to acquire high-resolution tomographic images with X-ray energies just above and below the absorption edge of an element. Concentration of the element could be calculated from the difference of these images with a correction using standard material. A 3-D Cs concentration map of a partially molten granite was obtained by this technique and compared with a 2-D element map produced by an electron-probe X-ray microanalyzer (EPMA), with respect to spatial and compositional resolution. A spatial resolution of about 20 μm was achieved by SP-μCT. The compositional resolution of ±2.5 wt% was achieved using the following two calibration processes of linear attenuation coefficients (LAC): (1) calibration based on the empirical relationship between theoretical LACs and observed CT values, and (2) the calibration of spatial variation of observed mass attenuation coefficients (MAC) due to X-ray energy shift using a standard material (Cs-bearing solution). Using the Cs2O map obtained by SP-μCT, 3-D image analysis was demonstrated, for example, connectivity of melt was calculated and it was found that 88 vol% of melt was connected in three dimensions in the sample. Furthermore, the possibility of 3-D diffusion studies by SP-μCT was discussed based on the spatial and compositional resolutions. This “nondestructive” and “3-D” mapping technique can reveal the internal compositional distribution of precious samples such as extraterrestrial materials and cultural assets, and can solve many 3-D issues such as material transport in geological and industrial materials.