The work stoppage by the GDL trade union hit long-distance and regional rail services as well as commuter S-Bahn train networks from 0100 GMT.
The strike -- the union's sixth bout of industrial action since September -- kicked off with freight services yesterday, added passenger trains today and is due to continue until early Monday.
But German rail operator Deutsche Bahn announced it had taken legal action in a bid to halt the walkout, saying it wanted to "do everything it could" to resume service.
About a third of intercity trains were running, while for regional and S-Bahn services it was between 15 and 40 per cent depending on the region, the company said.
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Politicians and industry groups have voiced fears about the impact of the strike, which is the longest in Deutsche Bahn's 20-year history, and will hit weekend celebrations for the 25th anniversary of the fall of the Berlin Wall.
Chancellor Angela Merkel insisted that the right to strike had to be carried out "responsibly" and "with a sense of proportion" in comments to reporters yesterday.
Late yesterday, the GDL union rejected an arbitration offer by Deutsche Bahn, which has slammed the latest walkout as "pure bullying".
GDL says Deutsche Bahn is stonewalling in talks over workers' demands for a five-percent wage hike and a shorter working week of 37 hours.
Union leaders also want to represent other groups of employees within Deutsche Bahn such as conductors, catering staff, dispatchers, and not just drivers.
Rail users at Berlin's main train station tried to stay patient despite the disruption during this morning rush hour.