Clarity refers to the internal flaws (inclusions) or the external blemishes of a stone. A flawless colored gemstone is rarer than a flawless diamond. However, even though clarity is important, it does not carry the premium that perfection has with diamonds. For example, a valuable emerald will be heavily included, as the natural process of emerald formation is violent, resulting in many natural flaws in even the most expensive of emeralds. In addition, lighter colored stones need to be cleaner, as their flaws show up more easily. Darker colored stones can hide their defects easier because of the depth of their color.

The location and the type of the inclusion or blemish is what are important with colored stones. For example, if there is a large crack on the surface of the stone, this can interrupt movement of light through the stone, and it may weaken the stone's durability. A large crack would probably detract from the stone's beauty and reduce its value. However, if the crack is small and positioned in a less noticeable area in the stone, then it will not affect durability, beauty, or price as much as a prominent flaw.

Inclusions may be also used to identify the origin of a stone. For example, Burmese rubies have unique inclusions such as unusual crystal formations that will identify the stone as having a Burmese origin. African rubies will not have these unique inclusions, but will contain their own unique inclusions, as the geological processes of their formation were different from their Burmese cousins.

Most gemstones will have tiny natural irregularities called inclusions. Most inclusions are not visible with the naked eye, usually you need to use 10X magnification to see these inclusions, however larger ones can be seen with the unaided eye. These irregularities may be substances such as an unfilled cavity, a small crystal, a fracture, or a growth pattern within the gem.