Charlotte Lewis, 48, a nurse at Montefiore Hospital was charged with four counts of failure to exercise control of a minor. She was arrested at the hospital.
Wilfred Lewis, 59, an MTA employee, was charged with endangering a child and four counts of failure to exercise control of a minor.
Prosecutors said the parents were not living in poverty but were raising their children in abject squalor.
The prosecutor called it a case of wanton abuse and neglect.
A Fed-Ex worker making a delivery to the apartment in the Kingsbridge section on Friday noticed the child by himself.
Parents of 5-year-old boy found home alone last night in despicable living conditions set to be arraigned shortly. Investigators say apartment in the Bronx was full of feces on the wall, infested with rats and roaches. Mom is nurse at Montefiore Hospital. Dad is an MTA employee. pic.twitter.com/rwZxGA3qTM— CeFaan Kim (@CeFaanKim) January 27, 2018
"FedEx came and dropped off a package and the kid opened the door," said neighbor William Villafane.
"When they asked for the parents, he answered that there was nobody."
The deliveryman then went out and hunted down a police officer. The child told police that his parents had not been home since Thursday night.
The parents have three other children - 13-year-old and 12-year-old girls and a 15-year-old boy.
The mother told police that they were in school and that she allowed the 5-year-old to stay home because he was sick.
She said she believed he was old enough to care for himself.
The apartment was full of human feces on the wall and was infested with rats and roaches. Prosecutors said they also found maggots and dead and live rodents.
One of the children was taken to the hospital with insects crawling on his body. A doctor indicated that one of the children had scabies from lice crawling under the skin.
There were also significant blood smears found in the apartment.
A large quantity of the smears were in the bathroom - on the floors and toilet. It is unclear where the blood came from, prosecutors said.
Neighbors said they were shocked by the conditions inside the apartment. "It's unbelievable knowing you're in a building that they got an apartment in those conditions," said Villafane. "I live on the third floor, we pass by it and we never knew that it was like that. I got a child, he's a year, and I try to keep things as clean as possible for him."
All four children are now in the custody of the Administration for Children's Services.
A judge set bail at $15,000 for both parents. They are expected to appear back in court in February.