The storms hit Rhineland-Palatinate and Hesse the hardest, felling dozens of trees, damaging 50 cars and ripping off roofs.
One driver was injured in Rhineland-Palatinate when he tried to avoid a fallen tree and drove into another tree.
Trains were delayed between Frankfurt am Main and Mannheim because of the storms.
The spa town of Bad Schwalbach in Hesse was particularly affected after being hit by a cyclone. According to police, 50 homes either had their roofs completely ripped off or damaged. Several trees fell onto the roof of a hotel in the village.
“It looks like a bomb has been dropped on the place,” one eyewitness said.
Click here for more pictures of the storm damage
Weather warnings are currently in place for Munich and southern Bavaria, the north German coast and the area around Erfurt in the centre of the country.
CLICK HERE for the weather forecast where you are