Quartz from different zones within five granitic pegmatites of the rare-element class from the Borborema Pegmatite Province in northeast Brazil were analysed for fourteen trace elements using laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS). The concentrations of Li (6–150 ppm), B (1–9 ppm) and Ge (1–23 ppm) in quartz show a positive correlation with Al (30–770 ppm). The concentrations of these elements increase from the border zone to the quartz core of pegmatites of the spodumene or lepidolite subtypes. The Ge concentrations in the quartz core are the highest so far reported in igneous quartz. In the less evolved pegmatites of the beryl-columbite subtype, the Al, Li, B, and Ge concentrations in quartz from all zones remain at the same level as the border and wall zones. The Ti concentrations in quartz from the core of the more evolved pegmatites are below 3 ppm (with Al >250 ppm), contrasting with 7–25 ppm (with Al <280 ppm) in samples from the border and wall zones of the less evolved and more evolved pegmatites. The concentrations of Al, Li, B, Ge, and Ti in quartz are therefore confirmed as good indicators of the degree of magma fractionation and analyses of pegmatite quartz cores can be used for exploration purposes to distinguish pegmatites with high metallogenic potential. Atoms of Li and Al are incorporated into quartz such that Li/Al ranges between 0.75 and 1.0. This suggests a coupled substitution of the form Si4+ ↔ (Li+ + Al3+). The other elements analysed either showed an erratic distribution (e.g. Be and P) or were below the respective limits of detection (Na, K, Rb, Ca, Sr, Mn, Fe) in most samples.