Quartz (trigonal, low-temperature α-quartz) is the most important polymorph of the silica (SiO2) group and one of the purest minerals in the Earth crust. The mineralogy and mineral chemistry of quartz are determined mainly by its defect structure. Certain point defects, dislocations and micro-inclusions can be incorporated into quartz during crystallisation under various thermodynamic conditions and by secondary processes such as alteration, irradiation, diagenesis or metamorphism. The resulting real structure is a fingerprint of the specific physicochemical environment of quartz formation and also determines the quality and applications of SiO2 raw materials. Point defects in quartz can be related to imperfections associated with silicon or oxygen vacancies (intrinsic defects), to different types of displaced atoms, and/or to the incorporation of foreign ions in lattice sites and interstitial positions (extrinsic defects). Due to mismatch in charges and ionic radii only a limited number of ions can substitute for Si4+ in the crystal lattice or can be incorporated in interstitial positions. Therefore, most impurity elements in quartz are present at concentrations below 1 ppm. The structural incorporation in a regular Si4+ lattice site has been proven for Al3+, Ga3+, Fe3+, B3+, Ge4+, Ti4+, P5+ and H+, of which Al3+ is by far the most common and typically the most abundant. Unambiguous detection and characterisation of defect structures in quartz are a technical challenge and can only be successfully realised by a combination of advanced analytical methods such as electron paramagnetic resonance (EPR) spectroscopy, cathodoluminescence (CL) microscopy and spectroscopy as well as spatially resolved trace-element analysis such as laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) and secondary-ion mass spectrometry (SIMS). The present paper presents a review of the state-of-the-art knowledge concerning the mineralogy and mineral-chemistry of quartz and illustrates important geological implications of the properties of quartz.