Combined cathodoluminescence (CL) and transmitted light microscopy were used to characterize quartz from flat and steeply dipping quartz veins and from veinlets in banded host rocks from the giant Muruntau Au quartz vein deposit, Kyzyl Kum Desert, western Uzbekistan. The CL examinations were carried out using a ‘hot-cathode’ CL microscope linked to a highly sensitive digital video camera. The multi-stage deformed flat quartz veins and the steeply dipping hydrothermal formations at Muruntau are characterized by quartz with different CL colours, internal structures and degree of secondary alteration. Primary growth zoning of quartz, indiscernible in conventional polarized light was found to occur only in steeply dipping veins. The bulk of the high-grade Au mineralized ‘central’ quartz veins is dominated by one generation of hydrothermal quartz; intense brecciation of these veins is indicated by the occurrence of fragments of zoned quartz crystals. Primary growth zoning in quartz may be revealed not only by variations in the intensity of blue CL and/or by primary fluid inclusions arranged within the zones, but also by secondary inclusions and recrystallization phenomena developed along boundary surfaces between the zones. Using the results from CL imaging and microstructural analysis of the quartz, fluid inclusions investigated earlier were assigned to genetic types; the evidence of probably primary inclusions is of considerable importance for further studies of the geochemical conditions during vein formation. Considering geological and mineralogical data, CL studies of vein quartz may help to reveal the history of precipitation, deformation and recrystallization processes in the Muruntau Au ore field.