A 3-year-old boy named Caleb was killed and his 2-year-old sister, Ellie, was critically injured.
The CSX spokesperson said the freight train hit the children at 10:30 a.m. in Portage, Indiana.
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Portage Police Chief Troy Williams said the little girl was airlifted to a hospital.
Police were still investigating how the children ended up on the tracks, which run along the edge of Woodland Village Mobile Home Park. A representative from the mobile home park said they lived there with their parents.
CSX train personnel told investigators they saw the children, honked and tried to stop but could not before striking them.
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An investigation is underway. CSX personnel were on the scene, assisting Porter County first responders.
"Our thoughts are with all involved in this tragic incident," CSX said in a statement.
The Associated Press contributed to this report.