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 and 100 injured, 50 of them seriously.
The drivers of both trains and two
train guards were among those killed, regional broadcaster Bayerischer Rundfunk
said, quoting police.
German Transport Minister Alexander
Dobrindt, who visited the scene, said it was a "horrifying sight".
"The drivers' cabs of both
trains are wedged into each other. One side of one train is completely torn
open," he told a news conference.
"The other train bored into it.
Obviously both trains crashed into each other at high velocity. We suspect that
both trains were travelling at around 100km/h (62mph)".
He added: "The site is on a
bend so we have to surmise that both train drivers had no visual contact before
the crash and therefore crashed into each other largely without braking."
Source: BBC
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