Holzkirchen is located on the Alpenvorland in the county of Miesbach. It was established as a Markt in the 13th century.
Holzkirchen was the location of one of the main transmitting stations for Radio Free Europe. Transmissions started in 1951 and provided the people of Eastern Europe with news from Western Europe. The transmitters had a strength of up to 250 Kilowatts, and in the 1980s caused a Tornado aircraft to crash near Oberlaindern, due to EMI problems of the aircraft's electrical systems. The Transmission also caused high cancer rates in the nearby community. It was so strong, the citizen could hear the radio programme through their faucets. After a community protest and a judge's ruling, the operator was persuaded to dismantle the station in 2004.
Nowadays Holzkirchen is well known as a location for pharmaceutical research and production. The European center of SANDOZ and HEXAL are located in the industrial zone.