Inbound train No. 636 hit a pedestrian around 10:45 a.m. near the Crystal Lake station, located at 70 East Woodstock Street. Police said no foul play is suspected.
Train service was restored in both directions around 1:45 p.m. Metra said riders should expect significant delays.
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Commuters are asked to listen for platform announcements or use Track Your Train on metrarail.com for the latest updates.
Officials also said the CTA will honor Metra tickets on the Blue Line from Rosemont to Chicago on Thursday.
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Earlier Thursday morning, inbound train No. 610 struck a vehicle at a five-way intersection near the Gladstone Park station. Avondale, Nagle and Somerset avenues, as well as five Metra tracks, meet at that intersection.
Police said a male in a northbound black Volkswagen with Illinois plates was crossing the tracks around 7 a.m. when the train hit the car. The driver was killed.
Officials from the Cook County Medical Examiner's Office removed his body from the vehicle. They may have to use fingerprints to identify him.
Investigators are looking at surveillance video from a camera on the other side of the tracks that may have recorded the crash. Officers climbed onto the roofs of nearby businesses to make sure there were no other victims.
People who live or work nearby said the intersection is tricky to navigate and that there have been fatal crashes there before.
The tracks were cleared and train service resumed around 11:10 a.m.
Both incidents remain under investigation.