The rail lines between Hanover and Hamburg and between Berlin and Wolfsburg are particularly affected, while passengers on the high speed inter-city ICE trains can expect the longest delays.
High wind speeds in the night caused trees to be blown over and branches to fall onto the overhead electricity cables. The worst damage was caused in Brandenburg and Lower Saxony.
Trains between Hamburg and Hanover have been redirected through Bremen. Passengers should reckon with delays of at least an hour.
Trains between Berlin and Frankfurt, Hanover and Braunschweig have been redirected through Wittenberge. Passengers can expect deals of an hour and a half.
The storms have also caused damage on roads in the east of the country, with Berlin, Saxony and Thuringia all affected.
Weather forecasters say the bad weather will continue throughout Monday, with strong winds and rain expected.