Two Pennsylvania SPCA officers had used a warrant to search the property after receiving a tip that two emaciated dogs were being kept at the house, in the 4800 block of North Front Street.
After finding the dogs alive - one in the basement and one in the backyard - the officers found the remains, police said.
A rifle also was found, but authorities did not know whether it was operational.
Police said they had not identified the owner of the house. The residence was so cluttered that the city Department of Licenses and Inspections will have to clear it, authorities said.
George Bengal, director of law enforcement for the Pennsylvania SPCA, said the agency's officers had entered the living room and found an altar constructed of about 50 primate skulls.
"This is a huge find," Bengal said. Those involved in the rituals "usually take the skull and the feet and the blood and drain the blood from the animal. They'll drink the blood and use the skull and feet as part of the altar."
Neighbors said that a man in his 50s or 60s lived at the property, but that they had not seen anyone there for months.
The windows were blocked by shades, and the man's truck was towed several days ago because the tags expired, said a neighbor who did not want to be identified.
SPCA officials will examine the remains to determine whether cruelty charges are warranted, said Liz Williamson, a spokeswoman for the Pennsylvania SPCA.
If the animals were killed "in line with how food animals are killed, then animal-cruelty charges would not be filed," she said.
Bengal said authorities had found animal remains in nearby park areas in recent years. Last month, animals that appeared to have been used in rituals were discovered near a bike path on Bingham Street near Roosevelt Boulevard in the Feltonville area.
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