The six splashed fake blood on themselves and members of the congregation as ushers tried to escort them out of Holy Name Cathedral, the Chicago Tribune reported.
The demonstration occurred as Cardinal Francis George delivered his homily.
"Even the pope calls for peace," the protesters chanted. "Even the pope calls for peace."
The congregation clapped when the cardinal answered, "And so should we all." Some members followed the protesters outside and yelled at them as they were being handcuffed.
Donte D. Smith, 18, Ephran Ramirez Jr., 22, Ryane Ziemba, 25, Mercedes Phinaih, 18, Regan Maher, 25, and Angela Haban, 20, were charged with felony criminal damage to property and simple battery.
The group released a statement saying they targeted the cathedral because of the large potential audience. They also attacked Cardinal George for meeting with President George W. Bush in January when the president came to Chicago.