It is thought that counties first formed in the beginning of the 2nd millennium as political and military unions of parishes.
In 1793 were formed Võru County in the south of Tartumaa, Viljandi County between Tartu and Pärnu counties, and Paldiski County in the west of Harjumaa.
Counties were re-established in 1 January 1990 in the borders of the Soviet-era regions.