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Pope welcomed Her Majesty and the Duke of Edinburgh, for what was described as a "warm and relaxed" encounter.
The Queen, dressed in a long black taffeta gown in line with Vatican protocol, arrived with the Duke at the Vatican in the rain at 1100 local time and took the lift up to the second floor.
Trumpets sounded and the royal procession moved slowly along the corridor into the Clementine Hall.
The Queen and the Duke were welcomed by John Paul II at the door of his private library.
The Queen then opened her speech with assurances of sincere friendship and good will.
She invited the Pope to her country in two years' time, but made clear this would not be a state visit but one "to the Roman Catholic community in Great Britain where some four million of my people are members of the Roman Catholic Church.
"We support the growing movement of unity between the Christian Churches throughout the world and we pray that your Holiness's visit to Britain may enable us all to see more clearly those truths which both unite and divide us in a new and constructive light."
In reply the Pope welcomed the opportunity of the forthcoming pastoral visit to the UK.
He said: "I render homage to the Christian history of your people, as well as to their cultural achievements.
"The ideals of freedom and democracy, anchored in your past remain challenges for every generation of upright citizens in your land."
They then held private talks and the Pope presented the Queen with a facsimile of the manuscript of Dante's Divine Comedy with its illustration of the Order of the Garter in the time of Edward IV.
In return she offered a book about Windsor Castle by St John Hope and two signed photographs.
After the talks, the Queen and Prince Philip walked out into the Clementine Hall and they went on to meet the Pope's Secretary of State, Cardinal Casaroli, at the home of the British Minister to the Holy See, Mark Heath.
The Queen's visit was seen as a big step towards forging relations with the Church Of England and the Roman Catholics.
In 1982 John Paul II was welcomed by Her Majesty two years later at Buckingham Palace during a historic visit to Great Britain.
The Queen visited the Vatican again in 2000 to mark the 20th anniversary of their first meeting.
The Pope reinforced their close ties over the years when he said: "Relations between the United Kingdom and the Holy See have not always been untroubled; long years of common inheritance were followed by the sad years of division.
"But in recent years there has emerged between us a cordiality more in keeping with the harmony of earlier times and more genuinely expressive of our common spiritual roots."
The Pope died at 2137 (1937 GMT) on Saturday 2 April 2005 after he failed to recover from a throat operation.
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