Police were called to a duplex on Amos Street around midnight, just east of Highway 288, and that is when the teen was found.
So far there are no suspects in custody, but four witnesses were taken downtown for questioning.
Officers are waiting for a judge to sign a warrant, then they can go in that duplex and search it.
Original report: 17-year-old shot in head on Houston's south side
Investigators told Eyewitness News they believe the gun is still inside.
Police said a group of kids, including the teen who was shot, broke into the duplex and have been squatting there for two weeks.
The property owner is not known, which is complicating matters. They are now searching for the owner as part of the process to get that search warrant.
A neighbor said she talked to one of the young women staying in the duplex, and this is what happened.
"Two little girls were in the living room," neighbor Ebony Hicks said. "The one that was in the living room said the guy who shot himself was on the counter playing with the gun, and it accidentally went off."
Hicks said she's only seen the young squatters in passing.
"I really didn't know them, they were kids, it was a hi and bye thing," Hicks said. "But the little guy who shot himself seemed like a sweet kid, always sitting outside, he was very quiet."
Police said the teen who was shot wasn't expected to make it at first, but he is hanging on to life at the hospital.
Report a typo to the ABC13 staff