Hillsboro is a city in Vernon County, Wisconsin, United States. The population was 1,302 at the 2000 census. The city is located within the Town of Hillsboro. Hillsboro is known as the Czech Capital of Wisconsin.
Hillsboro is located at 43°39′10″N 90°20′28″W / 43.65278°N 90.34111°W / 43.65278; -90.34111 (43.652843, -90.34133), along the West Branch of the Baraboo River.
According to the United States Census Bureau, the city has a total area of 1.2 square miles (3.2 km²), of which, 1.2 square miles (3.1 km²) of it is land and 0.04 square miles (0.1 km²) of it (2.44%) is water.