The fire was first reported about 5:30 a.m. at D & D Kennels, according to a statement from the DuPage County sheriff's office.
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A patrol deputy went into the building and was able to save 22 of the dogs, but 29 dogs died in the fire, officials said. No people were injured.
The kennel's owner, Garrett Mercado, lives on the property and discovered the fire when he returned to his home in the early morning. He did what he could to get the dogs to safety, but said the heat was too intense.
"The biggest thing is opening up the crates," Mercado said. "Trying to get the dogs out and moving and to follow me, and I couldn't even make it feet into my apartment. It was way too hot."
Mercado's fingers are blistered and his hair is singed, but he said that is nothing compared to the dogs that perished. He opened the kennel five years ago to board behaviorally challenged rescue dogs and train them for other people. Peter Cangelosi had 11 dogs there; only four survived.
"We take dogs no other rescue would take because they're challenged one way or the other," said Cangelosi, who's with Pets for Vets USA. "Garrett's the only one who can give this dog a second chance and then that dog gives one of our veterans a second chance."
Mercado also lost several of his own dogs but was overjoyed to see Capone, one of his client's dogs thought to be missing, recovered.
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"I didn't know he made his way out. I thought he was unidentifiable," Mercado said.
The dogs were brought to DuPage County Animal Services where they were given medical care and checked for microchips to be connected to their owners. Some of the deceased dogs were not able to be identified.
"We've had a few people have difficulty, breaking down and stuff like that, but for the most part, we have a job to do and know we have to do that to help the dogs and people, so we're gonna put on a brave face and keep striving ahead."
County Farm Road was closed between Jefferson Street and North Avenue, but the street was reopened by 12:20 p.m., the sheriff's office said. The cause of the fire remained under investigation by the DuPage County Fire Investigation Task Force.
Anyone who sees dogs running free in the area was asked to call 911.
The Sun-Times Media Wire contributed to this report