The incident was reported Sunday night near the area of 15th and Spurgeon streets, which appears to be a residential area.
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Police say the child - whose age wasn't released and was identified only as a toddler - was sitting in the backseat of a vehicle when she was shot.
Her parents rushed her to the hospital about two miles away from the crime scene after they realized she had been struck. She was initially listed in critical condition but eventually stabilized.
Video obtained by Eyewitness News shows a white Nissan Altima with bullet holes in the back and left side of the vehicle.
Toddler shot while sitting in vehicle in Santa Ana; investigation underway
It's unclear what sparked the shooting, but investigators do not believe the parents had anything to do with the shooting or the child's injury.
Authorities also said there's no indication the vehicle was intentionally targeted or that the shooting was the result of a road rage incident.
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Information about a suspect or suspects was not immediately released.
Meanwhile, Main Street is closed between 15th and 17th streets due to police activity.
This is a developing story. This article will continue to be updated as more information becomes available.