The head-on crash happened near Bad Aibling, a spa town about 60km (37 miles) south-east of Munich.
The trains' operator said both trains had partially derailed and were wedged into each other.
Emergency teams, some winched in by helicopter, worked for hours to free casualties from the wreckage.
Regional police said in a tweet (in German) that nine people had been killed. They said about 100 were injured, of whom 50 were seriously hurt.
The drivers of both trains and two train guards were among those killed, regional broadcaster Bayerischer Rundfunk said, quoting police.
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Rainer Scharf, of the German federal police, said that "given the severity of the accident, we believe the two regional trains collided head-on at speed that was not inconsiderable".
Regional train company Meridian said in a statement that "a tragic accident" had occurred on a single-track route between Rosenheim and Holzkirchen at about 07:00 local time (06:00 GMT).

Bernd Rosenbach, managing director of Bayerische Oberlandbahn, which operates Meridian trains, told reporters: "The accident is a huge shock for us. We are doing everything we can to help the travellers, relatives and workers."
Technical manager Fabian Amini added: "Our thanks go to the emergency services and workers who gave their help so quickly."
Other fatal German train crashes
- January 2011: 10 killed in Saxony-Anhalt when commuter train collides with goods train after driver runs through two signals
- February 2000: Nine dead when overnight train from Amsterdam to Basel crashes near Cologne
- June 1998: 101 killed when a high-speed train with a broken wheel derails and smashes into a bridge at Eschede in Lower Saxony
The scene of the crash is close to the Mangfall river in a hilly and densely wooded region. Casualties were being evacuated by boat and by helicopter.
Several hundred emergency services personnel were at the scene and rescue teams from nearby Austria were also helping, local media said.
By midday, police said all casualties had been removed from the wreckage.
The Munich blood bank issued an appeal for blood donors on its Facebook page(in German).
Although the trains were carrying commuters, local carnival holidays meant no schoolchildren were on board, according to reports.
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