"This is probably one of the largest casualty incidents in recent years (in San Francisco)," said Pat Gardner, a deputy chief with the San Francisco Fire Department.
Gardner said 20 people suffered moderate injuries. He described another 21 people as "the walking wounded." He said everyone who was injured remained conscious.
Witnesses said the westbound L train barreled into the K train as it emerged from a tunnel connecting downtown San Francisco to the city's western neighborhoods.
The front of the L train was smashed, while the K train suffered less damage. The operator of the L train was among the three with serious injuries.
Shin San, 15, said she got a phone call from her sister, Celene, who was on the L when it hit the K train.
"She said she was on the L and heard a boom," she said. "She saw glass windows shattered and a guy got his ear cut."
Shin said her sister hit her head but did not suffer serious injuries.
Witnesses said more than a dozen people sat on benches along the boarding platform after the crash, some of them holding bloodied heads. Most of the passengers were adults, many of whom had spent a sunny and breezy afternoon downtown.
Rescue workers set up a triage system to isolate the most severely injured, bandaging their heads and immobilizing their necks on stretchers before they were carted to waiting rescue vehicles.
"We thought a bomb went off," said Mike Burke, a San Francisco banker who lives near the crash site. He was walking past the station with his wife, Linda, after they went to the movies nearby.
"Lots of people (in the trains) were still sitting in their seats with their heads thrown back, stunned," Linda Burke said, adding that she saw people on the platform crying.
Dan Dudem, an unemployed mechanic and neighborhood resident, said he had just parked his motorcycle around the corner from the transit station when he heard the crash, and buildings shook.
"Everyone ran out of the stores to see what happened," he said. "I saw the front of the car crumpled."
The cause of the crash was under investigation.
Judson True, a spokesman for the San Francisco Municipal Railway, said investigators will look at "mechanical and human issues."
Saturday's crash was at least the third major transit accident in the U.S. since May.
Nine people were killed and more than 70 injured June 22 when a Metro train slammed into another train stopped on the tracks in Washington, D.C. The cause has not been determined but investigators say equipment that is supposed to detect stopped trains failed periodically in the days leading up to the crash.
On May 8, more than 50 people were injured when a Boston subway trolley plowed into another train. Authorities say the operator, Aiden Quinn, 24, went through a red signal while typing a text message on his cell phone.
Quinn was indicted earlier this month on charges of grossly negligent operation and was scheduled to be arraigned Monday in Suffolk Superior Court. He faces three years in prison if convicted.
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