German officials say one passenger remains missing, while more than 80 people were also injured - 18 of them are in a serious condition.
They say the crash happened during the morning rush-hour between the spa town of Bad Aibling and Kolbermoor in Bavaria.
Ambulances could not reach the site, which was heavily wooded with a steep hill on one side and a river on the other.
Police spokesman Jargen Thalmeier says helicopters were used instead to airlift the victims to hospitals.
"The injured people are being extracted from the passenger cars before they recieve emergency treatment. They are then taken by by helicopter to a nearby collection point close to a petrol station. From there, the injured are taken to nearby hospitals by ambulances."
The trains had been carrying about 100 passengers, mainly commuters.
Officials say that figure could have been higher if it wasn't for the holiday period.
Transport Minister Alexander Dobrindt was one of the first to visit the scene.
"Let me begin by saying it's a horrible site. The driver cabs of both trains are wedged into each other. One side of one train is completely torn open. The other train bored into it."
Mr Dobrindt says both trains must have been travelling at high speed.
"At the accident site, there is a speed limit of approximately 100 kilometres per hour. The stretch of railway track, in a bend in a curve, so one has to assume that the two train drivers had little - if any - visual eye contact of each other and so it is to be assumed that the collision took place without any braking."
The cause of the crash is not yet known.
However Alexander Dobrindt says an investigation has been launched to determine whether it was a technical problem or human error.
"Employees of the German federal railway authority are are on site to conduct an investigation. There are three black boxes in the two trains. Two of them were recovered. One is still in the wreckage of part of the train, but we expect that it will be possible to recover it during the course of the day."
The trains and track had been fitted with an automatic brake system.
It was introduced across Germany after ten people died in 2011 near Magdeburg when a train driver drove through two red signals.
Franz Brumado, from Bavarian Radio, says the system is supposed to stop trains going through a red light.
"This system is supposed to stop one of the trains or both of them after one has crossed the red line, or - as I was told - if there's two trains on a single track, both trains had to be stooped."
Chancellor Angela Merkel has expressed shock and sent her condolences to families of the victims.
Share
