variety of banded, colored quartz, 1560s, from French agate, from Latin achates, from Greek akhatēs, the name of a river in Sicily where the stones were found (Pliny). But the river could as easily be named for the stone.
Earlier in English as achate (early 13c.), directly from Latin. The Elizabethan sense of "a diminutive person" is from the small figures cut in agates for seals, etc., and the notion of smallness is preserved in typographer's agate (1838), the U.S. name of the 5.5-point font called in Great Britain ruby. Meaning "toy marble made of glass resembling agate" is from 1843 (colloquially called an aggie). Related: Agatine.