A staunch defender of the role of the church in Greece, he died at his home in Athens, only months after plans for a liver transplant in the United States were cancelled.
"He was an enlightened church leader whose work brought the church closer to society, closer to modern problems and to young people," Prime Minister Costas Karamanlis said in a statement.
Condolences poured in and crowds of black-clad mourners gathered at his Athens home, where he died, as well as the Metropolitan Cathedral where his funeral will be held after a three-day wake.
"It is like I have lost my father," an elderly woman praying outside the church told Greek TV. Christodoulos courted controversy from his first reformist days at the helm of the church through to a conservative U-turn that drove away many supporters.
"I am sad for the loss of the person even though I didn't agree with his policies," said Irini Politou, 32, an office clerk.
Christodoulos grudgingly agreed to a landmark visit by Pope John Paul to Greece in 2001 that marked a turning point in relations between the Catholic and Orthodox Churches since the Great Schism of 1054 that split Christianity.
Born Christos Paraskevaidis in northeastern Greece in 1939, he became the youngest head of the church when he was elected to the top post in 1998, following the death of his predecessor.
He stunned Greeks by calling on young people to return to the church "as you are, earrings and all," and cracking jokes during his weekly sermons, instantly raising his institution's popularity and profile.
But his laid-back approach soon gave way to a bitter feud with the then socialist government over new ID cards, which according to EU directives no longer listed a person's religion.
His frequent tirades against the EU and European culture, his reference to Turks as "barbarians", labelling gays as being "handicapped", and his growing public involvement in foreign policy issues chipped away at his popularity.
He was diagnosed with cancer in June 2007.
"The way he dealt with his disease and imminent death moved us, sending a unique message of courage and dignity," Greek President Karolos Papoulias said in a statement.