Pope Benedict XVI held Mass in Israel's Josaphat Valley, beneath the Mount of Olives
Pope Benedict XVI has been visiting sites in Jerusalem holy to Muslims, Jews and Christians on the second day of his visit to the Holy Land.
He visited the Dome of the Rock in Jerusalem, becoming the first pontiff to see the site, and then the Western Wall, one of Judaism's holiest places.
He said Mass in the Josaphat Valley and is later to pray at the reputed site of Christ's Last Supper.
A row has broken out over the German-born Pope's time in the Hitler Youth.
A Vatican spokesman appeared to contradict the pope's own admission that he was once a member.
There has also been criticism from Israeli politicians and commentators about the Pope's comments on the Holocaust.
The Pope is meeting both Israeli and Palestinian leaders during his tour.
Israel has beefed up security for the trip in an operation named "White Robe", with tens of thousands of law-enforcement officers deployed and entire sections of Jerusalem shut down.
The Pope began the day's visits at the Dome of the Rock, located on the Temple Mount - a site sacred to all three monotheistic religions.
Katya Adler, BBC News, Jerusalem
The Mass in the picturesque and historically charged Josaphat Valley is not well attended.
The 5,000 tickets for the Mass were sold out. Olive trees were temporarily removed to make room for the anticipated crowds of enthusiastic pilgrims. Yet few have actually turned up.
The adoration that followed Pope Benedict's predecessor during his visit to the Holy Land nine years ago seem to be conspicuously absent.
The Middle East is also a sadder and darker place.
John Paul came here in March of the millennium year - before the 11 September attacks, before the US-led invasion of Iraq, before the second Palestinian uprising and Israel's tougher controls on Palestinians.
Ahead of Pope Benedict's visit few Christians said they believed he could or would improve their lives much. Their absence here today, if for that reason, speaks volumes.
He removed his shoes according to Islamic custom when entering a holy site, and met the Grand Mufti of Jerusalem, Mohammed Mohammad Hussein.
"Here the paths of the world's three great monotheistic religions meet, reminding us what they share in common," said the Pope.
The mufti called on the Pope to end Israeli "aggression" against Palestinians.
There was no live television coverage of the visit because of a dispute between Israeli and Palestinian broadcast companies, said the BBC's David Willey, who is travelling with the Pope.
Pope Benedict then moved to the nearby Western, so-called Wailing, Wall where he met Israel's chief rabbis.
The wall is part of the retaining wall of the Temple Mount, dating back to a time when a Jewish temple stood there.
He said the visit gave him the opportunity to reiterate the Catholic Church's commitment to "a genuine and lasting reconciliation between Christians and Jews".
The Pope placed a written prayer into a gap in the wall, before standing in silence with his head bowed.
His prayer asked the "God of Abraham, Isaac and Jacob" to send "peace upon this Holy Land, upon the Middle East, upon the entire human family".
At the Mass in Josaphat Valley, he said the departure of many Christians in recent years was a "tragic reality".
"In the Holy Land there is room for everyone," he said to applause.
"I urge the authorities to respect, to support and to value the Christian presence here."
The pontiff will later visit the site reputed to be where Jesus took his Last Supper before his crucifixion and resurrection.
Hitler Youth controversy
Media coverage of the trip and debate in Israel have pointed up the fact that the German-born Pope was, like other German children, enrolled in the Hitler Youth during World War II.
POPE IN THE MIDDLE EAST
Monday Arrives in Israel, meets President Shimon Peres
Tuesday Visits the Dome of the Rock and the Western Wall. Celebrates Holy Mass in Josaphat Valley
Wednesday Visits Bethlehem, visits refugees, meets Mahmoud Abbas
Thursday Mass in Nazareth, talks with Benjamin Netanyahu, meets Franciscans
The Speaker of Israel's parliament, Reuven Rivlin, described Pope Benedict as a "German who joined the Hitler Youth and... a person who joined Hitler's army".
Vatican spokesman Rev Federico Lombardi said on Tuesday: "The Pope was never in the Hitler Youth, never, never, never."
His remark appeared to contradict the Pope's own words in his 1997 memoirs, Salt of the Earth.
"As a seminarian, I was registered in the HY [Hitler Youth]," he said then. "As soon as I was out of the seminary, I never went back."
The Rev Lombardi sought to make a distinction between the anti-aircraft auxiliary corps the Pope was enrolled in towards the end of the war and the Hitler Youth, which he described as a "corps of volunteers, fanatically, ideologically for the Nazis".
This page is best viewed in an up-to-date web browser with style sheets (CSS) enabled. While you will be able to view the content of this page in your current browser, you will not be able to get the full visual experience. Please consider upgrading your browser software or enabling style sheets (CSS) if you are able to do so.