Jesse Shipley was 17 when he died in a car crash in 2005.
Andre and Korisha Shipley say they had no idea his brain was removed during an autopsy until some of the teen's classmates at Port Richmond High School spotted it floating in a jar on a field trip.
After the incident, the city returned the brain and the family disinterred their son from a cemetery so they could bury him with the missing organ.
A city doctor said the brain had been kept for additional tests related to the autopsy.
A city attorney says officials are "evaluating our legal options" for resolving the case.