In the formation of an ordinary agate, it is probable that waters containing silica in solution -- derived, perhaps, from the decomposition of some of the silicates in the lava itself -- percolated through the rock and deposited a siliceous coating on the interior of the vapour-vesicles. Variations in the character of the solution or in the conditions of deposit may cause corresponding variation in the successive layers, so that bands of chalcedony often alternate with layers of crystalline quartz. Several vapour-vesicles may unite while the rock is viscous, and thus form a large cavity which may become the home of an agate of exceptional size; thus a Brazilian geode lined with amethyst and weighing 35 tons was exhibited at the Dusseldorf Exhibition of 1902.

The first deposit on the wall of a cavity, forming the "skin" of the agate, is generally a dark greenish mineral substance, like celadonite, delessite or "green earth," which are rich in iron probably derived from the decomposition of the augite in the mother-rock. This green silicate may give rise by alteration to a brown oxide of iron (limonite), producing a rusty appearance on the outside of the agate-nodule. The outer surface of an agate, freed from its matrix, is often pitted and rough, apparently in consequence of the removal of the original coating. The first layer spread over the wall of the cavity has been called the "priming," and upon this base zeolitic minerals may be deposited.
Many agates are hollow, since deposition has not proceeded far enough to fill the cavity, and in such cases the last deposit commonly consists of quartz, often amethyst, having the apices of the crystals directed towards the free space so as to form a crystal-lined cavity, or geode.
On the disintegration of the matrix in which the agates are embedded, they are set free. Being a siliceous material, which is extremely resistant to the action of air and water, they remain as nodules in the soil and gravel, or become rolled as pebbles in streams.

A Mexican agate, showing only a single eye, has received the name of "cyclops agate." Included matter of a green, golden, red, black or other colour or combinations embedded in the chalcedony and disposed in filaments and other forms suggestive of vegetable growth, gives rise to dendritic or moss agate (named varieties include Maury Mountain, Richardson Ranch, Sheep Creek and others). Dendritic agates have beautiful fern like patterns on them formed due to the presence of manganese and iron ions. Other types of included matter deposited during agate-building include sagenitic growths (radial mineral crystals) and chunks of entrapped detritus (such as sand, ash, or mud). Occasionally agate fills a void left by decomposed vegatative material such as a tree limb or root and is called limb cast agate due to its appearance.
Turritella agate is formed from fossil Turritella shells silicified in a chalcedony base. Turritella are spiral marine gastropods having elongated, spiral shells composed of many whorls. Similarly, coral, petrified wood and other organic remains or porous rocks can also become agatized. Agatized coral is often referred to as Petoskey agate or stone.
Certain stones, when examined in thin sections by transmitted light, show a diffraction spectrum due to the extreme delicacy of the successive bands, whence they are termed rainbow agates. Often agate coexists with layers or masses of opal, jasper or crystaline quartz due to ambient variations during the formation process.

Other forms of agate include carnelian agate (usually exhibiting redish hues), Botswana agate, blue lace agate, plume agate (such as Carey, Graveyard Point, Sage, St. Johns, Teeter Ranch and others), tube agate (with visible flow channels), fortification agate (which exhibit little or no layered structure), fire agate (which seems glow internally like an opal) and Mexican crazy-lace agate (which exhibits an often brightly colored, complex banded pattern).
In Islam, agates are deemed to be very precious stones. According to tradition, the wearer of an agate ring, for example, is believed to be protected from various mishaps and will enjoy longevity, among other benefits. In other traditions agate is believed to cure the stings of scorpions and the bites of snakes, soothe the mind, prevent contagion, still thunder and lightning, promote eloquence, secure the favour of the powerful, and bring victory over enemies. Persian magi are also known to have prized agate rings in their work and beliefs.
The Shia Book of collected prayers, Mafatih Al-janan, quotes the fifth Shia saint Imam Muhammad al-Baqir on agates, as such:
"Whosoever endures the night 'til sunrise wearing an agate ring on his/her right hand, before seeing or being seen by any human that morning, turns the agate ring toward the palm side of his/her hand, and while looking at the gem recites the 97th chapter of the Qur'an followed by this prayer [specified], then the God of the Universe shall grant him/her immunity on that day from any danger that falls from the sky, or rises up to it, or which disappears into the earth, or rises out of it, and he/she shall remain protected by the power of God and the agents of God until dusk." (p1212 of version by Haj Sheikh Abbas Qomi)