Other gemstones contain trace amounts of impurities, which give them color.  A good example of this is the Ruby.  It is colored red by trace amounts of the element chromium.   This small amount of impurity gives the stone its color.  The well-known blue sapphire is colored by the presence of the elements titanium and iron. In this particular case, both of them are required to give the sapphire its blue color. If no impurities are present in a sapphire gem, the stone is completely without color.  Fancy colored sapphires in green, yellow, orange and other shades are colored by various impurities or combination of impurities. Most of these coloring impurities are a metal atom, so gemstones which can accommodate a variety of different metal atoms like corundum (sapphire and ruby) are often found in a large variety of possible colors and shades.

Another common source of color is what is called a color center.  A color center is an imperfection in a crystal often caused by damage to the crystal structure.  Many gemstones are actually colored by natural irradiation.  Trace amounts of radioactive materials present in common rocks will, over many thousands of years expose a gem to enough radiation that it's Crystal structure will be slightly damaged. That slight damage causes certain wavelengths of light to be absorbed, resulting in coloration within the stone.  In many these of these gems, heat or additional radiation can lighten or darken, or even change the color of the stone. Blue Topaz is an example of a gem colored by a color center crystal imperfection.

For some gems which contain multiple sources of color, the colors are combined and what is seen by the viewer is the total of the colors together.  For example, with turquoise, which is naturally blue, the addition of iron as an impurity adds a yellow coloration, turning the turquoise which contains some iron a green color (blue plus yellow is green).

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