Houston police officers responded to a shooting call just after 8 p.m. Wednesday on Glenbrook United Methodist Church's property on Glen Valley Drive and Wilmerdean Street.
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There was some confusion, though. The injured boy was actually part of Centro Cristiano Pentecostal, a small Hispanic congregation.
Centro Cristiano leases a building from Glenbrook United Methodist Baptist Church for services.
The pastor said about 10 people were inside when the shot rang out. The bullethole was still visible on the side of the building when Eyewitness News visited the church.
The pastor, who didn't want to show his face on camera, said his prayer service on Wednesday night was interrupted by a loud boom.
"We all lifted our heads up when we heard the noise. A boy started crying and telling his mom his arm hurt, saying something hit him," the pastor explained in Spanish. "Then, we realized it was a gunshot."
First-responders located the 11-year-old boy and rushed him to the hospital, where he was stable, police said.
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Investigators said the boy was inside the church, lying down and reading a book, when the shooting happened.
Nearby neighbor Robert Estrada said he watched the aftermath unfold from his front lawn.
"I asked the lady what happened, and she told me, 'Somebody shot through, and it hit the little boy who was sitting down,' and I said, 'Wow.' But he was fortunate. It could have killed him, I suppose," Estrada said.
He adds that the sounds of gunshots aren't uncommon in the area.
His neighbor, Jesus Carillo, said a bullet almost went through his home four years ago.
"They hit the tree, and I heard the gun, and I actually heard the bullets fly next to us, and then the guy - about five minutes later - this guy comes running into my garage with blood spatter," Carrillo said.
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Officers walked the perimeter of the church and found several shell casings about 300 feet away from the building, police said.
Detectives are working to determine if the shooting was a targeted attack.
"We don't have problems with anyone," the pastor claimed.
Investigators are not calling it a hate crime during the immediate wake of the shooting, but they are questioning if it has anything to do with noise complaints the church received about two months ago.
Police didn't have any information about the suspect or suspects in the shooting.