Chalcedony is not scientifically its own mineral species, but rather a form of Quartz in microcrystalline form. However, the name is an old name, and almost all mineral reference guides and collectors distinguish Chalcedony separately from Quartz. In the gem trade, the name Chalcedony usually describes only white or blue Chalcedony, to distinguish it from the multicolored banded variety Agate and other unique varieties of this mineral.

Chalcedony is quite varied in its formation habits. It sometimes occurs in geodes, lining the cavity with mammilary blobs. Its Agate variety is also found in geodes, commonly lining the outer layer underneath the larger Quartz crystals. Chalcedony also forms pseudomorphs after organic material. A well-known example is petrified wood, in which the wood has been completely transformed into Chalcedony. In the Petrified Forest National Monument in Arizona, an entire forest was transformed into petrified wood. Remains of this ancient forest can be seen in the huge silicafied logs that are found in the area.

Another well-known pseudomorph is Chalcedony after coral. In the Tampa Bay in Florida, coral has been chemically replaced by Chalcedony, and its original form is preserved. Another famous Chalcedony pseudomorph is Tiger's Eye. This popular variety has very unique optical properties in the form of a bronze sheen that is caused by the fibrous mineral Crocidolite that was chemically replaced into Chalcedony through pseudomorphism.

Impurities are frequently present in Chalcedony. They may form a moss like growth in the mineral, forming what is known as Moss Agate. Another example is Dendritic Agate, a variety of Chalcedony containing manganese oxide impurities that form fabrications resembling trees. These forms of Agate are not true Agates, since they lack the banding.

For additional information, see the gemstone section on Chalcedony.