To understand trace radionuclide (uranium) migration occurring in rocks, a granitic batholith located at the Korea Atomic Energy Research Institute (KAERI) site was selected and investigated. The rock samples obtained from this site were examined using mineralogical methods, including scanning electron microscopy (SEM) and electron probe microanalysis (EPMA). The changes in the distribution pattern of uranium (U) and small amounts of trace elements, and the mineralogical textures affected by weathering, were examined. Based on the element distribution analyses, it was found that Fe2+ released from fresh biotite is oxidized in short geological time, forming amorphous iron oxides, such as ferrihydrite, around silicate minerals. In that case, the amorphous ferrihydrite does not show distinct adsorption for U. However, as it gradually crystallizes to goethite or hematite, the most U-rich phases were found to be associated with the secondary iron oxides having granular forms. This evidence suggests that the geological subsurface environment is favorable for the crystallized iron oxides to keep their structures more stable for a long time as compared with the amorphous phases. There is a possibility that the long residence of U which is in contact with the stable crystalline phases of iron may finally lead to the partial sequestration of U in their structure. Consequently, it seems that Fe-oxide crystallization can be a dominating mechanism for U uptake and controls long-term U transport in granites with low U contents.