After the overnight clashes in the slum of Imbaba, residents turned their anger toward the military. Some said they and the police did almost nothing to intervene in the five-hour frenzy of violence.
Six Muslims were among the dead, said Egypt's state-run news agency.
The bloodshed began Saturday around sundown when word spread around the Imbaba neighborhood that a Christian woman who married a Muslim had been abducted and was being kept in the Virgin Mary Church against her will.
The report of the kidnapping, which was never confirmed by local religious figures, sent a large mob of Muslims toward the church. Christians created a human barricade around the building, and clashes erupted. Gunfire sounded across the neighborhood, and witnesses said people on rooftops were firing into the crowd.
Crowds of hundreds of Muslims lobbed firebombs at homes, shops and the church. Residents say Christians were hiding inside.
Across the Nile River, in downtown Cairo, clashes broke out on Sunday afternoon. Muslim youths attacked Coptic Christian protesters, Christian activist Bishoy Tamri said.