For decades, the U–Pb isotope system of zircon is routinely used in geosciences for the determination of intrusion ages of felsic magmatic rocks. It is, however, well-known that zircon and the related U–Pb isotope system may be influenced by secondary hydrothermal alteration and new (hydrothermal) zircon growth. As a result, age determination may yield meaningless or alteration ages. An example is given here for intensely altered late Paleozoic granitoid rocks from the Muruntau area, Central Kyzyl Kum, Uzbekistan. Pb–Pb single grain evaporation and U–Pb SHRIMP isotope systematics of zircon from six granitoid rocks yield roughly consistent results defining ages ranging between 288 and 303Ma. At first glance, these ages may be understood as intrusion ages of the magmatic rocks hosting the zircon. However, there is an apparent contradiction between the sequence of the measured U–Pb SHRIMP ages and the relative age sequences established in the field. Evaluation of data from comprehensive mineralogical and petrological studies reveals that the U–Pb system of magmatic zircon is complicated by inheritance in I-type granitoids, recrystallization, new hydrothermal zircon growth, and subsequent secondary alteration. Widespread albitization of the granitoids led to the formation of new, U-rich, hydrothermal zircon forming overgrowths on older grains or even new whole single crystals. Later alteration events caused direct and (apparent) reverse U–Pb isotope discordances. These late disturbances of the U–Pb system are mainly due to widespread sericitization. Consequently, precise concordant U–Pb zircon SHRIMP ages around 290–294Ma defined for U-rich, largely undisturbed crystal areas constrain the timing of albitization rather than that of the intrusion. The reliability of the concordant U–Pb SHRIMP ages measured on U-rich zircon is confirmed by a U–Pb SHRIMP age of hydrothermal monazite (292±8Ma). This monazite associates with extremely U-rich zircon (U–Pb SHRIMP age: 291±3Ma) in a sample of the Murun granite recovered beneath the giant Muruntau gold deposit by super-deep drilling. Obviously, detailed mineralogical studies are important for a correct interpretation of zircon ages when hydrothermal alteration and late re-mobilization of zirconium and uranium were significant as often observed in areas with intense ore mineralization. The extensive Au mineralization found at Muruntau is similar in age to albitization but apparently somewhat younger. Likewise, the intrusion age of Permian granites is at least somewhat older than the hydrothermal zircon ages confirmed by U–Pb ages of monazite. It is, however, difficult to constrain further granite intrusion ages based on presently available data.