The chemical and structural alteration of metamict zircon crystals from a 619317 (2σ) Ma old, post-tectonic granite in the southern part of the Eastern Desert, Egypt was studied. The crystals show simple oscillatory growth zones with metamictization-induced fractures, which provided pathways for fluid infiltration. Electron and ion microprobe analyses reveal that metamict, i.e. U and Th-rich, areas are heavily enriched in Ca, Al, Fe, Mn, LREE, and a water species, and have lost Zr and Si as well as radiogenic Pb. These chemical changes are the result of an intensive reaction with a low-temperature (120– 200°C) aqueous solution. The chemical reactions probably occurred within the amorphous regions of the metamict network. During the zircon-fluid interactions the metamict structure was partially recovered, as demonstrated by micro-Raman and -infrared measurements. A threshold degree of metamictization, as defined empirically by an α-decay dose, Dc, was necessary for zircons to undergo hydrothermal alteration. It is proposed that Dc marks the first percolation point, where the amorphous domains start to form percolating clusters in the metamict network and where bulk chemical diffusion is believed to increase dramatically. The time of the hydrothermal alteration is determined by a lower intercept age of a U-Pb SHRIMP discordia of 17.9+6.9−7.4 (2σ) Ma, which is in good agreement with an apatite fission track age of 22.2+5.4−4.8 (2σ) Ma. The hydrothermal alteration event occurred contemporaneously with the main rifting phase of the Red Sea and widespread low-temperature mineralizations along the Red Sea coast.