The GIA system has 3 classes of gems based upon  the expected degree of clarity in the cut gems.  

GIA type I stones  are gems that are expected to have very few inclusions and are generally eye clean.  GIA type II gems typically  are somewhat included, while type III gems are ALWAYS included.  This means that a type III gem, such as Emerald, can be rated at VS-1 or VS-2 and have significant inclusions, while an aquamarine, a type I gem of the same clarity, would be rated SI-2 or I-1. Type I gems are expected to be cleaner (i.e. higher clarity) than type II or III.  The higher the type the cleaner the stone is expected to be.  Type I gems include: aquamarine, morganite, heliodor,  tanzanite, blue zircon, and green tourmaline.  These gems are expected to be flawless or near flawless.  Type II gems include: alexandrite, corundum (ruby and sapphire), spinel, amethyst, citrine, ametrine, blue and paraiba tourmaline,  and garnet.  These gems usually have inclusions and this is normal and expected, even at high clarity ratings.  Type III gems include emerald, red beryl, paraiba, red, pink, and watermelon tourmaline.  These gems are ALWAYS included to some degree.  The absence of inclusions indicates possible synthetic, rather than natural, origin.

  •  GIA type I stones require eye clear or near eye clear clarity to be acceptable.  Type II stones are more likely to have inclusions and clarity rules are much less stringent than is the case with type I stones.  Type III stones are expected to be included; flawless or near flawless stones (e.g. VVS stones) are extremely rare and found mainly in museums and other private collections of very rare specimens.  The average 'high quality' stone in the Type III group has significant inclusions and these are taken into account in the clarity ratings.  In other words, emeralds, which are Type III, almost always have significant inclusions and this is simply assumed when clarity is graded. Aquamarine, on the other hand, is a Type I stone, and is expected to be eye clean, if not flawless.  Aquamarines are, thus, expected to be eye clean, wherein Emeralds are simply expected to exhibit 'jardin' or 'garden,' in reference to the garden of inclusions inside the gemstone. An emerald and an aqua might BOTH have a VS rating for clarity, but the emerald has significant 'jardin' with many inclusions and the aqua is near eye clear with no inclusions visible without magnification.  The difference is that the emerald is Type III, while the aquamarine is type I.