A scanning electron microscope based cathodoluminescence technique utilizing a novel collector system reveals complex internal heterogeneities within granitic quartz grains. The technique overcomes the low intensity and limited variation in cathodoluminescence generated by quartz, which hamper conventional cathodoluminescence analysis. Detailed images of zoning patterns in quartz are comparable to those observed in minerals such as feldspar, and attributed to a combination of progressive growth, boundary layer effects and mineral-melt disequilibria produced during fluctuations in melt composition and temperature during the crystallization interval. We attribute such mineral-melt disequilibria to open system, mixing behaviour in the granite plutons sampled.