While it's unknown what the pair discussed, speaking to Egyptian media after the meeting, the Pope said: "Prince Mohammed spoke a lot of his affection for the Copts."
He said the heir to the kingdom of Saudi Arabia also invited him and all Copts to visit his country.
The talks are being seen as part of a softening of Saudi Arabia's ultra-conservative Muslim position.
The Crown Prince of Saudi Arabia visited the Coptic Pope today in Cairo and invited him to visit Saudi Arabia.
— Johnnie Moore ن (@JohnnieM) March 6, 2018
A new day is coming in the Gulf. pic.twitter.com/Xxaztce0tP
Egypt has been hit by a series of church attacks by groups linked to Islamic State in recent years.
A bombing near to the cathedral where the meeting took place saw 25 people killed in 2016.
Prince Mohammed is carrying out a series of foreign visits.
He's expected to travel to the UK later this month.
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