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"Right now, this is a death investigation," said Arden Wiltshire from the San Bernardino County Sheriff's Department.
Authorities said the train hit the body just after midnight between the San Bernardino and Riverside stations in the community of Grand Terrace. The train immediately stopped after impact and remained on the tracks.
Police waited until full light before investigating exactly what happened.
"We're not sure what this person was doing on the tracks," Wiltshire said.
Authorities said it was difficult to figure out how he died because of the impact.
Metrolink trains 803, 805 and 807, which run from San Bernardino to Oceanside, were canceled after the incident. Two tracks were closed, but at 7:45 a.m., one of the two tracks were reopened.
Metrolink officials said trains from San Bernardino to Los Angeles were not affected.
The male victim has been identified, but authorities have not notified next of kin yet.