Practically all aspects of agate genesis generate debate. The time is ripe to clarify the most important enigmas concerning the environments of formation of agates and the related famous amethyst geodes of Brazil and Uruguay. Agates form over a wide range of temperatures, from those of basaltic and andesitic melts (about 1100 °C) down to about 50 °C, and at rather low pressures. Their formation in liquid mafic magmas is indicated by a correlation between (1) the orientation of amygdules and the inclination of onyx banding in them and (2) the attitude of amygdules in the lava flow layers. The correlation arises because lava moves at a different rate close to and far from the upper and lower rims of a flow. The alkaline supercritical fluid fills gas vesicles in lavas and dissolves silica, mainly, from ambient lava or rock to produce a silica sol. If the pressure on the fluid causes percolation of water from amygdules, the sol coagulates on the walls of the vesicle to form a concentric lining. If the pressure in amygdules falls below the maximum osmotic pressure of a sol (about 0.1 MPa for a silica sol), percolation of fluid stops, and coagulation leads to the formation of horizontal onyx banding. Multiple repetitions of precipitation of various gel layers can be caused by overlapping fresh flows upon the cooling older agate-bearing lava flow. In a submarine setting, phase separation of the fluid and the formation of a film of gel between vapor (or diluted solution) and brine stimulate the osmotic processes, which result in growth of hollow membrane tubes and branching moss-like arrays at the bottom of amygdules. Some agates exhibit numerous channels as a result of repeated extrusion of fluid or gel from inner zones to the periphery of amygdules that were compressed under the burden of new flows. Previously, such channels were interpreted to be feeding channels for silica supply in amygdules. Periodic compression of amygdules after percolation of fluid from them requires no additional supply of silica because the volume of the amygdules is reduced in proportion to the loss of fluid. The concentric and horizontal banding and mossy textures of agates from the lithophysae of felsic volcanic rocks were created during active volcanism as well. The agates from dissolution-induced cavities in carbonate rocks and the famous amethyst druses of Brazil and Uruguay formed at the moderate temperatures associated with low-grade burial metamorphism, as indicated by the lack of moss textures and onyx banding.