Chicago police said the boys are 3 and 8 years old.
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Both children were expected to be OK Thursday morning.
The 3 year old who was transported to Comer Children's Hospital was listed in good condition.
CPD said that shooting happened near the 700-block of East 93rd Street just before 10 p.m. in Burnside.
Police believe the 3 year old was asleep in his bed when shots were fired from outside the home, injuring the child in his elbow. At least 10 bullet holes pierced the home.
RELATED: 'Random act of violence': 12-year-old boy critically injured in Near West Side shooting, police say
Neighbors said some of those bullets even made it into their downstairs apartment, piercing the living room walls.
Just about 15 minutes before that shooting, an 8-year-old boy was shot inside his West Woodlawn home near the 3600-block of South Rhodes Avenue.
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He was grazed by a bullet that pierced the wall, as gunfire erupted outside the home.
He was not taken to the hospital, but this continues the startling trend of minors shot in the city this year.
"I heard the shots from my house this time, and I would never have thought that a child would be on the bad end of those bullets. But right now Chicago is on the bad end of those bullets," Pastor Donovan Price said.
Just a couple days ago, a 12 year old was critically hurt when he was shot in the head on the Near West Side.
He is still in the hospital.
Police said it happened near West 21st Place and Wood Street.
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The boy and his uncle were walking back from a store when witnesses said two people fired shots from a nearby alley.
The uncle fired back.
"This is obviously a very tragic case. The uncle is a 21 year old. He's not affiliated at all with any gangs. He's a valid CCL holder, and actually returned fire in this incident, doesn't believe he struck anybody," Chicago Police Deputy Chief Brendan Deenihan said.
Chicago police have three people in custody, who they say are affiliated with gangs, but it's still not clear if they're the suspects of this shooting.
According to ABC7 Chicago data, there have now been 255 minors shot in Chicago this year. Thirty three were killed.