Mühlhausen is a city in Thuringia, Germany.
Mühlhausen, German for "mill houses", may also refer to:
- German naval ship Mühlhausen, in service with the German Navy
- other places in Germany:
- Mühlhausen (Affing), village in the municipality Affing near Augsburg, Bavaria, Germany
- Mühlhausen (Kraichgau), municipality in Baden-Württemberg, Germany
- Mühlhausen am Neckar, a town now part of the Stuttgart conglomerate in Baden-Württemberg
- Mühlhausen bei Schwenningen, community of Villingen-Schwenningen in southern Baden-Württemberg, Germany
- Mühlhausen, Middle Franconia, in the district of Erlangen-Höchstadt, Bavaria
- Mühlhausen, Upper Palatinate, in the district of Neumarkt, Bavaria
- places outside Germany:
- Mühlhausen an der Moldau, the former German name of Nelahozeves, Czech Republic
- Mühlhausen, the former German name of Milevsko, Czech Republic
- Mühlhausen in Ostpreußen, the former German name of Młynary, Poland
- Mühlhausen (Kreis Preußisch Eylau), today Gvardeyskoye, Kaliningrad Oblast, Russia
- Mülhausen, the German name for Mulhouse, France
- Mulhausen, Bas-Rhin, village in France