By Christian Fraser, BBC News, Castel Gondolfo, Rome
It was the first time the Pope had been able to put in person an apology which he has now made in public on three occasions.
"Christians and Muslims must learn to work together," he said, "in order to guard against all forms of intolerance and to oppose all manifestations of violence".
The meeting shows the Pope is keen to foster closer ties with Islam. He has already stated that the two religions share one God.
The Pope's November trip to Turkey still looks like it will go ahead and in light of the recent controversy it perhaps takes on added significance.
Today the Pope has received a sympathetic ear - but his first visit to a predominantly Muslim country may well be a much tougher proposition.
In May 2004, 10 new countries joined the club, eight of them former communist states from Central Europe.
The unprecedented speed of this next expansion, albeit the second instalment of the last one, partly explains why the reaction in many European capitals is, as one British columnist has put it: "Oh no, do we have to?"
"The indigestion from that biggest-ever enlargement is putting the whole enlargement process at risk," says Hugo Brady of the Centre for European Reform.
Hugo Brady draws parallels with a "difficult period" which followed the accession of a "somewhat belligerent and nationalist" Greece in 1981, not long after it emerged from dictatorship.
The period did not last long, he says. EU membership helped to seal the country's full transition to democracy, and it quickly became a valued member of the union.
The EU has in fact committed itself to accepting Balkan states and Turkey when they meet the membership conditions.
One thing most observers agree on is that enlargement will go slower in future, if not immediately, and that the rules will be applied more strictly, even if they are not changed.
The unprecedented monitoring that both Bulgaria and Romania will be subjected to after accession and the severe penalties they will face if found wanting - such as a restriction of farm aid - are probably a taste of things to come.
Pictures courtesy of BBC News online.