Mineral isochron dating is a frequently used geochronological tool. One of its assumptions is that the minerals grow over a time period that is small compared to the half-life of the radiogenic isotope system used. In recent years, increasing analytical precision has promoted the use of the short-lived U-series isotope system in order to date young crystallisation events. Three whole-rock zircon U–Th isochrons from the 26.5 ka Oruanui eruption in the Taupo Volcanic Zone, New Zealand, yield pre-eruptive model ages of 5.5±0.8 ka, 9.7±1.7 ka and 12.3±0.8 ka for the sub-63 μm, 63–125 μm and 125–250 μm zircon size fractions, respectively. This suggests that in this case the assumption of instantaneous crystal growth breaks down. Instead, the U–Th data may be explained by continuous zircon growth over a period of ∼90 ka. However, cathodoluminescence shows that crystals are typically composed of an euhedral core surrounded by a sector-zoned euhedral rim, and the U–Th data can also be modelled by mixing an older (∼27 ka model age) population of zircon crystals with a young zircon rim that formed shortly prior to eruption of the Oruanui rhyolite. This indicates that detailed petrographic studies are critical for deciphering the histories of prolonged crystallisation in the magmatic environment. It is concluded that conventional U-series mineral isochrons may underestimate the age of the onset of crystallisation by more than an order of magnitude. In future, microanalytical techniques will lead to significant advances in the understanding of crystallisation processes and timescales.