It took Cook County Sheriff's investigators about five hours to seize the animals. Two dead animals were also found.
Owner of the Dazzle's Painted Pasture Animal Rescue/Sanctuary, Dawn Hammill, 41, is charged with multiple counts of neglect and cruelty to animals.
The animals were seized Friday night in south suburban Tinley Park, Ill., after the sheriff's office received some tips.
Investigators did surveillance first, then obtained a search warrant for the shelter on Friday. They found dozens of animals living in unhealthy conditions in barns, trailers and sheds that were often unheated. They were often without food and water.
Among the animals were dogs with skin conditions, cats with respiratory problems and many animals with eye and ear infections. Eight puppies also had diseases.
Police found a 3-and-a-half-year-old miniature horse that died in the barn, along with a dead Himalayan cat.
"There was nothing wrong with what I did," Hammill told ABC7 on Saturday. "I'm not God, I cannot stop animals from dying. We did everything we could to save them. Unfortunately, they did pass. We handled their remains and we've done what we were supposed to do."
Hamill has been charged with eight counts of neglect of owners' duties and two counts of cruel treatment.
"Not one of those animals were malnourished. They come into us in horrible condition and we rehab them," Hamill said.
In all, police removed 63 dogs, 31 cats and six rabbits. Horses, sheeps and llamas were also found.
Executive Director of the Animal Welfare League in Chicago Ridge, Linda Estrada was there when Hamill was arrested.
"She did not have enough human care for these animals. They were not cleaned properly. They were not living in an environment that any animal should," said Linda Estrada, executive director of the Animal Welfare League in Chicago Ridge.
Estrada is caring for the domestic animals at the Animal Welfare League in Chicago Ridge. She says Hamilll actually thanked her and investigators for intervening when they did.
"She thanked us for helping her downsize," Estrada said. "Her intent was good. It just went out of control."
Hamill founded her non-profit as a no-kill shelter in 2006. She was procuring animals online and taking them in from other places as well. She offers up animals for adoption for a fee.
"I believe to this minute I did the right thing for those animals. If anybody says any different, that is their opinion," Hamill said.
Hamill's next door neighbor Al Yursis says she was devoted to her animals, but he believes she just got overwhelmed.
"She's out there from early morning til late at night. Everyday. So I would never think that, there is definitely no abuse," Yursis said.
Hamill is out on bond Saturday night. She plans to fight the charges.
She told ABC7 she was too busy to talk on-camera because she's trying to comply with orders placed on her by investigators.
Officials at the Animal Welfare League say they will be working with her in the future to make sure the animal population on her property remains manageable.
Once the rescued animals are well, they will be up for adoption.