Color in gemstones results from a complex series of interactions. The passage of light through a mineral substance is subject to the way the atoms in the mineral are arranged, so with every system in which the mineral crystallizes in there are alterations in the color of the mineral. The wavelength usually does not change but rather the atoms may be selective about what wavelengths or colors the will permit to pass. If the atoms are arranged so that only red may pass, then red is all that emerges. Consequently, the gemstone appears transparent or partially transparent red. This is a major source of color in transparent stones. If the stone stops the passage of all light it looks opaque and black. Black is the absence of a visible wavelengths.

Gemstones are sometimes found to be different colors in different deposits. Fluorite, for example, is found at various mines in specimens of blue, green, pink, yellow, brown, purple, and black. Absolutely pure fluorite is colorless, so any color in it must come from something added to it that is not typical of pure fluorite. Colored minerals like this are called allchromatic, which means the color is due to traces of impurities or to defects in the arrangement of atoms in the structure.

To say that all the reaction between light and gemstones is due to the kinds of atoms present and their arrangement would be an oversimplification. There are certain other color effects that are caused by structural defects or by the presence of relatively large impurities. One example is interference, a phenomenon that creates two part light waves that are out of synch with each other. The resulting combination is seen by the observer as a different mixture of wavelengths from the original ray or by definition and appearance a different blend of color.