Animal experts began removing the animals from the house Tuesday afternoon.
The animals include dogs, cats, lizards, turtles, birds, chinchillas, rabbits, ferrets, hamsters and rats.
Between 40 and 60 cats were taken out, along with at least 22 dogs.
2 cats and one chinchilla were found dead.
"The conditions inside are deplorable," said Regina Benfante of the Suffolk SPCA.
The home's owner has signed the animals over to the Suffolk County SPCA, which is removing them for triage and treatment.
The house is apparently owned by a 70-year old woman who lives there with her daughter.
It was a neighbor complaining about barking dogs that led the SPCA to launch the investigation five days ago.
It took that long to make contact with the woman, who let investigators in Tuesday.
"There's so many, is what made the conditions so bad. She just became overwhelmed," said Maureen Schneider, director of the Brookhaven Animal Shelter.
The Yaphank Fire Department arrived on the scene to vent the house because of the stench.
The house has been condemned.