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The combination of scanning electron microscope–cathodoluminescence (CL), fluid inclusion analysis and high-resolution electron probe microanalysis of Al, Ti, K and Fe in vein quartz has yielded results permitting a greater understanding of the complex mineralisation of the Central Oyu Tolgoi and Zesen Uul porphyry-style deposits, southern Mongolia. These data demonstrate the relationship between quartz precipitation, dissolution and ore deposition as the mineralising fluid chemistry changed through time. Four major quartz generations are identified in the A-type veins from the stockworks of both the Central Oyu Tolgoi (OTi to OTiv) and Zesen Uul deposits (ZUi to ZUiv). Despite differences in the associated alteration and mineralisation style, the observed CL textures and trace element signatures of the quartz generations are comparable between deposits. The OTi and ZUi stage formed both the primary network of A-type veins and pervasive silicification of the host rock. Using the Ti-in-quartz geothermometer, crystallisation temperatures for OTi and ZUi of between 598°C and 880°C are indicated. The main stage of sulphide mineralisation was accompanied by the dissolution of pre-existing quartz (OTi and ZUi) and precipitation of a weakly luminescent generation of quartz (OTii and ZUii) with a low Ti content, reflected in a calculated temperature drop from approximately 700°C to 340°C in Central Oyu Tolgoi and 445°C in Zesen Uul. OTii and ZUii stage quartzes show high and variable Al concentrations. The next stage of quartz in both deposits (OTiii and ZUiii) forms a fine network of veins in cracks formed in pre-existing quartz. OTiii and ZUiii quartz contain measurable fluid inclusions of moderate salinity (3–17.1 wt.% NaCl eq.), entrapped in the temperature range 256°C to 385°C. OTiii and ZUiii are not related to any sulphide mineralisation. The final OTiv and ZUiv stages are characterised by quartz–calcite micro-breccias that penetrate the A-type veins. Based on the calculated entrapment temperatures, the OTiv/ZUiv stage crystallised between 212°C and 335°C, and the quartz is characterised by elevated but variable Al and Fe contents. The CL and trace element signatures of the OTi to OTiii and ZUi to ZUiii stages of the two Mongolian porphyries show similar features to those observed in porphyry-style deposits from other regions. This suggests that a common sequence of quartz crystallisation occurs during the formation of early veins in many porphyry copper systems.