Pure quartz, traditionally called rock crystal or clear quartz, is colorless and transparent or translucent, and has often been used for hardstone carvings, such as the Lothair Crystal. Common colored varieties include citrine, rose quartz, amethyst, smoky quartz, milky quartz, and others. These color differentiations arise from chromophores which have been incorporated into the crystal structure of the mineral. Polymorphs of quartz include: α-quartz (low), β-quartz, tridymite, moganite, cristobalite, coesite, and stishovite. 

The most important distinction between types of quartz is that of macrocrystalline (individual crystals visible to the unaided eye) and the microcrystalline or cryptocrystalline varieties (aggregates of crystals visible only under high magnification). The cryptocrystalline varieties are either translucent or mostly opaque, while the transparent varieties tend to be macrocrystalline. Chalcedony is a cryptocrystalline form of silica consisting of fine intergrowths of both quartz, and its monoclinic polymorph moganite. Other opaque gemstone varieties of quartz, or mixed rocks including quartz, often including contrasting bands or patterns of color, are agate, carnelian or sard, onyx, heliotrope, and jasper.

Citrine is a variety of quartz whose color ranges from a pale yellow to brown due to ferric impurities. Natural citrines are rare; most commercial citrines are heat-treated amethysts or smoky quartzes. However, a heat-treated amethyst will have small lines in the crystal, as opposed to a natural citrine's cloudy or smokey appearance. It is nearly impossible to differentiate between cut citrine and yellow topaz visually, but they differ in hardness. Brazil is the leading producer of citrine, with much of its production coming from the state of Rio Grande do Sul. The name is derived from the Latin word citrina which means "yellow" and is also the origin of the word "citron". Sometimes citrine and amethyst can be found together in the same crystal, which is then referred to as ametrine. Citrine has been referred to as the "merchant's stone" or "money stone", due to a superstition that it would bring prosperity.

Citrine was first appreciated as a golden-yellow gemstone in Greece between 300 and 150 BC, during the Hellenistic Age. The yellow quartz was used prior to that to decorate jewelry and tools but it was not highly sought after.