Abstract The characterisation of quartz using trace element geochemistry and electron paramagnetic resonance measurements has been tested for different generations of quartz veining in the multi-stage hydrothermal vein system at Cowarra. Quartz closely associated with gold mineralisation can be distinguished from earlier and later quartz generations in the mineralised environment, and both types can be distinguished from regional, barren quartz veins. These separate stages of quartz veins are also recognised from their fluid inclusion characteristics. Geochemical differences in the quartz partly reflect the presence of minor mineral inclusions, particularly sulfides and arsenopyrite. The study highlights the importance of understanding the paragenetic sequence of quartz vein development in a mineralised environment and the need for careful, thorough sampling before attempting geochemical and EPR characterisation of quartz as an exploration technique.