After a heatwave over the three-day holiday weekend, thunderstorms, strong winds and heavy rain pounded the western state of North-Rhine Westphalia, causing Duesseldof airport - the third-largest in the country - to close for about an hour.
Three people were reported to have died in the state capital when a tree fell on a garden shed in which they were sheltering. Three other people who took refuge in the shed were injured, two of them seriously.
A cyclist, aged around 50, died in nearby Cologne after being hit by a falling tree that police said was probably struck by lightning, and another cyclist died in Krefeld. A sixth person died in the town of Essen from a suspected heart attack while trying to clear a street.
Ten incoming flights to Duesseldorf airport were diverted and 10 other flights were cancelled, with winds of up to 93mph recorded.
The airport opened again late on Monday night.
Early yesterday, national rail operator Deutsche Bahn said numerous train services were still suspended and trains that were operating would face severe delays.
Fallen trees blocked some streets in Duesseldorf, where trams and underground trains were also stopped due to damaged overhead lines. Some residents also reported power cuts.
The storm front moved further north-east and the German Meteorological Service issued weather warnings for other parts of the country, including Hanover and Bremen.