Police went to the home in the 4800 block of North 9th Street around 9:15 a.m. Thursday to serve a domestic abuse warrant against a woman there.
Officers said once they went inside, they found the house was in a "deplorable" condition, with feces scattered around.
Investigators say there was no working toilet in the home, with waste in containers and on the floor. Police say it may be human waste, but will test it to make sure.
Police then called the Special Victims Unit and DHS.
The children, girls ages 1, 3 and 4, have been taken to the hospital to be checked out.
One veteran sergeant told Action News he's never seen anything so bad, noting that one girl was covered in feces.
Both the mother, 24-year-old Lakeeshanaye Overton, and father, 26-year-old Soyika Eldermire, were taken into police custody to be questioned about the care of their girls.
Police say both are now charged with recklessly endangering another person and endangering the welfare of the child.
Police say the couple owns the home. They also noted that the father works as a security guard at Children's Hospital of Philadelphia.
Philadelphia Police Captain Jack Flemming described what he saw inside: "It looked a little un-kept. The smell was a little bit tough to take. However, we'll let Special Victims take a look at it and together with the Department of Human Services and let them make a decision on how the conditions were."
From the street nothing seems amiss about the home. There are flowers in the front window, and through the open door a large TV can be seen.
Block Captain Arlene Booth reacted to news of the conditions inside the home, telling Action News, "It disturbs me. You know, I mean because ... I'm speechless. All I can say is I'm speechless."
Eldemire and Overton were arraigned overnight, the Philadelphia District Attorney's Office said. Bail for Eldemire was set at $10,000 and bail for Overton was set at $7,500.