Crystals come in all shapes, sizes and colors. The variation in color is generally caused by the chemical elements involved while the crystal is being formed.
Quartz
Most crystals are colored quartz. Quartz changes colors because of the chemicals found in the surrounding environment when it is forming.
Chemicals
Different colors are created by different chemicals. Amethyst for example has iron deposits built into its crystalline structure giving it a purple cast. Crystals with sulfur built into their structure have a yellow cast.
Growth Imperfections
Some coloration, like that found in smoky quartz, are the result of growth imperfections. These imperfections effect the way the crystal reflects light, and so change the appearance of coloration.
Light
Part of the color we see when looking at a crystal is light. When light enters a crystal its spectrum is broken apart, and part of it is absorbed while other parts are reflected. This reflection and absorption changes the apparent color of the crystal.
Cutting
The shape of a gem is often altered, and facets added, to enhance the color of the crystal. The planes of the cut crystal alter the way in which it interacts with light, and so alters the color.
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