Amethyst is the violet variety of quartz; its chemical formula is SiO2.

In the 20th century, the color of amethyst was attributed to the presence of manganese. However, since it is capable of being greatly altered and even discharged by heat, the color was believed by some authorities to be from an organic source. Ferric thiocyanate was suggested, and sulfur was said to have been detected in the mineral.

More recent work has shown that amethyst's coloration is due to ferric iron impurities.Further study has shown a complex interplay of iron and aluminium is responsible for the color.

On exposure to heat, amethyst generally becomes yellow, and much of the citrine, cairngorm, or yellow quartz of jewelry is said to be merely "burnt amethyst". Veins of amethystine quartz are apt to lose their color on the exposed outcrop[citation needed].

Synthetic amethyst is made to imitate the best quality amethyst. Its chemical and physical properties are so similar to that of natural amethyst that it can not be differentiated with absolute certainty without advanced gemological testing (which is often cost-prohibitive). There is one test based on "Brazil law twinning" (a form of quartz twinning where right and left hand quartz structures are combined in a single crystal[3]) which can be used to identify synthetic amethyst rather easily. In theory however it is possible to create this material synthetically as well, but this type is not available in large quantities in the market.