Some 300 workers walked off the job in Nuremberg, Hamburg, Munich and Cologne in an ongoing wage dispute with Deutsche Bahn.
Regional and long-haul stretches in the state of Bavaria were the most heavily affected, with some 150 workers in Nuremberg and Munich laying down their tools in the early hours of the morning.
According to Deutsche Bahn, Nuremberg has had the most problems, but otherwise the strike has caused “few adverse effects” on traffic.
But news agency DDP reported that there were delays and isolated cancellations in the Rhineland cities of Cologne and Düsseldorf.
More workers are planning to stage a temporary strike in Hamburg, Saalfeld, Berlin and Magdeburg as the day goes on, but city S-Bahn trains will not be affected.
Unions Transnet and GDBA called the trikes a "warning signal for the employer" amid gridlocked talks over better work schedules, the unions said. While several hundred workers with different specialties were taking part in the strikes, their goal was not to cripple rail service in the country, they said.
On Wednesday Transnet head Alexander Kirchner accused Deutsche Bahn of "stonewalling" the unions after a third round of talks in Frankfurt. Both unions are fighting for at least 12 free weekends per year and better nightshift regulations for some 130,000 workers, in addition to a 10 percent pay raise.
Deutsche Bahn has offered a one percent pay raise for 2009 and 2010, and a one-time bonus. Insiders had said the company would make a new deal attempt on Wednesday, but the unions reported they had not received another offer.
The unions said they would not strike again between Friday and Monday out of respect for passengers.
Customers affected by delays can get their tickets refunded until February 15, Deutsche Bahn said, adding they had set up a toll-free hotline for strike information on: 08000 99 66 33. Passengers can also check their website for news of delays and cancellations.
Train conductor union GDL is also wrangling with Deutsche Bahn over a 6.5 percent pay raise for its 12,000 workers, but does not yet have any strikes planned.