There are two categories of zircon, "high zircon" and "low zircon". The high zircon has better transparency and more consistent index of refraction and specific gravity. The "low zircon" has traces of uranium or thorium in the structure, and the radio active decay of these trace elements destabilizes the crystal structure making their physical properties less reliable. Low zircon is a bit of a collectors item but usually not used in jewelry. (The radiation is usually low enough that they do not cause physical harm.)

The most common zircon is the brown to red-orange zircon and may be quite pleasing but the most popular color today is the blue zircon. Funny, the blue zircon is usually created by heat treating some brown zircons. Zircons are commonly heat treated to improve color, or the clarify of the stone. The blue is sky blue and they are similar in color to sky blue topaz, but easily identified due to their double refraction, and much greater color dispersion.

The orange to light yellow-brown stones are sometimes called "honey zircon" and may be quite attractive. They are often the least expensive, although many are used to create blue or clear zircons through the heat treating process. Thus many honey colored zircons never make it to market as honey colored stones.

There is a red zircon which is highly prized if it is not too dark. In most gemstones, dark red is usually desirable, but in the case of zircons dark red stones lose some of the color play associated with high dispersion and index of refraction. Some of the red to red-orange stones are called "hyacinth".

The rarest color is green and is a collectors stone although not a jewelers item to any great extent.