Witnesses said some 500 conservative Islamists known as salafists gathered at the Saint Mina Church in the Cairo suburb of Imbaba demanding to take custody of a woman they said had converted to Islam.
A shouting match ensued between church guards and neighbours and the Islamists. The verbal clash soon developed into a full fledged confrontation where the two sides exchanged gunfire, firebombs and stones.
Another church in Imbaba, The Virgin Mary, was set on fire by angry crowds later.
"I just left one young man dead inside the church," one Christian witness told journalists at the scene.
Authorities deployed large numbers of soldiers and police, backed by armoured vehicles, to the area. The army fired shots in the air and used tear gas to separate both sides, witnesses said.
A security source put the death toll at 12 and said 186 had been wounded, according to the state MENA news agency. The director of the health department in Giza province, Abdel-Halim al-Behairi said five had died and 54 had been wounded. He told MENA that three of the wounded were in serious condition.
Interfaith relationships often cause tension in Egypt, where Christians make up about 10 percent of its 80 million people.
The Grand Mufti of Egypt Ali Gomaa, a senior Islamic religious figure, called for calm. "All Egyptians must stand shoulder to shoulder and prevent strife," he told MENA.
He also urged the military council to stop anyone from meddling with the security of Egypt.
Christians complain about unfair treatment, including rules they say make it easier to build a mosque than a church.
In response to the deadly sectarian clashes in Imbaba on Saturday night Egypt’s Supreme Council of the Armed Forces issued communiqué number 48 on their official Facebook page stating that 190 have been arrested and will face military trials.
The statement warns of sectarian strife and its dangers to the country’s well-being and stability and called on all revolutionary youth and people to stand together with religious scholars of both religions against sectarianism.
The statement also read that attacks on houses of worship of any religion will be severely punished.
Sectarian clashes have increased after Egypt’s revolution that ousted the autocratic Mubarak regime that had been ruling Egypt with a tight fist for 30 years.
Last year Egypt saw more than its usual share of sectarian strife, and a rights groups has said such clashes have been on the rise. Muslims and Christians had been brought together during the protests that ousted Mubarak.