The drivers of two separate vehicles died at the scene.
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The toddler was flown to the hospital via LifeFlight and later died of his injuries, according to a tweet from Community Volunteer Fire Department.
Fort Bend County deputies say the crash happened just before 1:15 a.m.
Houston TranStar cameras captured flames coming from the cars.
"This is a pretty horrific crash," Sgt. Danny Beckworth with Fort Bend County Sheriff's Office said. "The family shouldn't have to go through this."
According to investigators at the scene, one car caught fire, and the flames spread to the second one.
A white Audi SUV driving westbound was struck head-on by a black Hyundai sedan traveling the wrong way on the tollway, deputies said. The driver of the Hyundai was driving eastbound in the westbound lanes.
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By the time firefighters arrived on scene, one of the cars was fully engulfed in flames.
A 31-year-old male driving the Hyundai and his 2-year-old passenger were both killed. A preliminary investigation revealed that the driver may be the toddler's uncle.
A female driver in the Audi was also killed. She was trapped inside her vehicle when it caught fire, deputies said.
"Right now, we're working with the toll road authority to try and get the cameras to see where they might have gotten on the tollway the wrong way," Beckworth said. "That, right now, is still under investigation."
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Deputies do not believe the toddler was restrained in a car seat at the time of the crash.
"I don't think the child was restrained. Not in a car seat," Beckworth said. "The seatbelt had been cut to get him out, but there is not a car seat."
An ABC13 photographer working overnight heard the accident as he was traveling on the feeder road. He said he saw debris fly over the freeway, but didn't know what happened until it was reported over the police scanners.
"I was on my way to another assignment... I was on the feeder road when I heard this loud explosion. I didn't know if something had blown up or something," ABC13 photographer Marvin Suggs said. "Then this smoking debris came off the freeway and landed in front of my vehicle. So I'm dodging debris."
The Westpark Tollway westbound at FM 1464 is closed.
For updates on this crash, follow Charly Edsitty on Facebook, Twitter and Instagram.