Any animals placed for adoption must get a clean bill of health first.
Town officials say the owner of the puppies, identified as Eileen Monroig, is being charged with cruelty to animals and numerous town code violations.
Eyewitness News reporter Emily Smith has more.
Police say 56 little puppies were taken out, one-by-one, from a home officials describe as a puppy mill. They say it was the worst possible environment they've seen in years.
The home is described as a place of filth and darkness, and scores of puppies were carted out in little cages after being crammed together in a basement, five or six in one box, according to Suffolk County police.
"They had no water, no ventilation, they were living their own filth," Suffolk police sergeant Kevin McKeon said.
"They were all small breeds," said Roy Gross, of the Suffolk SPCA. "There were some Shitzus, miniature poodles, pekingese, yorkies, what else is in there, I really don't know."
The puppies were taken out and placed in a Suffolk SPCA bus. Now, many are looking for new homes.
"I worked K-9 for four years," Suffolk police sergeant Kevin McKeon said. "This is a the worst I've ever seen."
Police say Monroig is a woman in her 60s who drives a 2008 Lexus with vanity plates that say "Puppy4U."
As officials rescued the little dogs, neighbors watched from the middle of the street. Many were in disbelief.
"She's a very nice woman," neighbor Melissa Ortiz said. "I've met her a few times. She's good-hearted, very sweet."
The owner may be facing criminal charges for reported animal abuse and neglect. She could spend a year in jail. Officials say neighbors complaining of the smell coming from the house is what tipped off the investigation. The goal now is to get all the puppies into new homes.