Colors are the result of the absorption of certain wavelengths of visible light. When a specific wavelength of light passes through a gem, or is reflected from its surface, what we see are the wavelengths that are not absorbed. So, when we see a red gemstone, in actual fact that gemstone is every color but red. The absorption of certain light wavelengths in some gemstones is caused by the inclusion of impurities; these impurities add color to minerals.

The color in Amethyst was originally thought to be uniquely due to the presence of the mineral impurity of iron. But the impurity theory did not add up when Amethyst was clearly observed to have an unstable coloration, which faded after exposure to heat and light sources. The fading of color in this way is contradictory to the impurity theory, as other gem types such as Ruby are routinely heated up to as much as 2000 degrees Celsius, which instead of weakening the color intensifies it. Moreover, heated at high temperatures Amethyst was observed to loose it's purple nuance altogether, shifting to a yellow color. In fact, this is the source of much of the world's Citrine.

All gemstones, at some point in their billion year lives, have been exposed to radiation in one form or another. In the case of Amethyst, the forming of 'Color Centers' by natural radiation took place when high-speed electrons pierced the mineral's atomic crystal structure, hitting smaller molecules and displacing them. When these molecules were displaced from their regular positions, their place was taken by one of the electrons, which became trapped in the vacant space. This trapped electron absorbed light energy, which caused it to get excited and jiggle. The light energy was then dissipated through the motion of the excited electron, and with it a subset of color wavelengths from the light energy was used up. What we see as the color of an Amethyst is what light energy wavelengths remain that have not been used up by the excited electron. This is the creation of a 'Color Center,' the phenomenon that gives Amethyst, topaz and some colored diamonds their color.