In Saint Mark's Cathedral, where Coptic Pope Tawadros II led the mass, worshippers passed through three metal detectors as policemen and soldiers stood guard in the sprawling compound and on the streets outside.
Two Islamic State group suicide bombers had struck two churches north of Cairo last Sunday, killing 45 people in the worst attack on Copts in recent memory.
Police cordoned off roads leading to the cathedral compound, where another suicide bomber had attacked last December, killing 29 people.
The Islamic State group, which claimed all three bombing, has threatened more.
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Following the Palm Sunday attacks, the church had said it would scale back Easter celebrations.
"Tanta and Alexandria created a big shock, for all of Egypt," Coptic Church spokesman Boulos Halim said.
Easter, which along with Christmas is one of Christianity's most important events, marks what followers believe was the resurrection of Christ on the third day after his crucifixion.
In Egypt, Copts break a 55-day fast abstaining from all animal products following Saturday's mass.
"In a week like this it becomes especially pertinent because we see the direct effect of that sin," he told AFP by phone.
Sunday's bombings, the deadliest on Copts in recent memory, were the latest in a series of attacks against the Christians who make up around 10 percent of Egypt's 90 million people.
In Sinai, where IS's Egypt affiliate is centred, jihadists killed seven Copts in January and February, forcing dozens of Christian families to flee the peninsula.
"I don't think the churches are any emptier, in fact they might be fuller," said Bishop Angaelos.
"But it just means people leave home knowing they are a target, but that doesn't stop them."
One Copt who gave his name only as John said he will attend Easter mass despite the threat of attacks.
He plans to go to a church in the relative safety of the capital, but admitted "if I were somewhere else outside of Cairo, like a village, I would not want my relatives to go and I would be worried about attending".
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