Braving pelting rain, the German-born pontiff joined Vienna's chief rabbi, Paul Chaim Eisenberg, in quiet prayer before an austere stone memorial honoring the 65,000 Viennese Jews who perished in Nazi death camps and others burned at the stake in the 1400s after refusing to convert.
Earlier Friday, Benedict told reporters on his flight to Austria that the poignant and highly symbolic stop at Vienna's Judenplatz, or Jewish Square, was intended to show "our sadness, our repentance and our friendship to the Jewish people."
In 1938, the city's Jewish community was one of the world's largest and most vibrant with 185,000 members. Today, there are fewer than 7,000.
Alluding to the nation's Nazi past, President Heinz Fischer conceded in a greeting to the pope that Austria had "dark hours in its history."
Benedict, making his seventh foreign trip in two years as pope, professed his affection for the mostly Catholic country, telling Austrians he felt "a vivid sense ... of being at home here in your midst."
"This cultural space in the heart of Europe transcends borders and brings together ideas and energies from various parts of the continent," Benedict told Fischer, Chancellor Alfred Gusenbauer and other dignitaries at a military welcome hastily moved inside an airport hangar because of the poor weather.
Austria borders Eastern Europe and its melting pot of Catholics, Orthodox Christians, Muslims and Jews.
But the pope, who visited and vacationed here often as a cardinal, faced a challenge: many Austrian believers, disgusted by clergy sex scandals and deeply resentful of a government-imposed church tax, have grown cold - and tens of thousands have left the church altogether.
Benedict's trip underscored the difficulties the Vatican confronts across Europe, where cathedrals are empty as disillusioned believers question the relevance of faith in the postmodern era.
Reflecting the anti-pope sentiment held by some Austrians, Socialist youth organizations planned a demonstration Friday afternoon in central Vienna to protest the pontiff's conservative stance on homosexuality, gay marriage and other issues.
Cardinal Christoph Schoenborn, the alpine nation's top churchman, appealed to his countrymen not to let cynicism "detract from the joy of this visit." It is the first papal visit to Austria since the late Pope John Paul II made a pilgrimage in 1998.
"Your visit honors us and makes us happy," Fischer told Benedict.
Several hundred cheering pilgrims huddled beneath umbrellas and sang "O Happy Day" at an opening ceremony on Vienna's lavish Am Hof square. The ceremony was delayed after microphones failed and a giant screen went black. But the wet crowd remained in good humor, applauding as the pope grinned and waved, and some broke into song.
"I'm coming to see the pope because I think he's on a mission to save the world," said Madueke Ugokwe, 35, a Nigerian native living in Austria.
Security was heavy for Benedict's visit, with more than 3,500 police officers and soldiers and 50 aircraft deployed to protect him. The Interior Ministry said the measures were taken even before this week's thwarted terrorist plot in Germany.
In his arrival remarks, the pope praised those who do volunteer work, saying "whoever looks to his neighbor - seeing him and helping him - looks to Christ and serves him."
Later Friday, at the former imperial Hofburg Palace, Benedict was to address Austrian authorities and foreign diplomats based in Vienna. Benedict said he would use the speech "to take another look at our present and our future."
On Saturday, the pope holds an open-air Mass to commemorate the 850th anniversary of the founding of Mariazell, a famous shrine to the Virgin Mary about 100 kilometers (60 miles) southwest of Vienna.
The Vienna Archdiocese said 33,000 pilgrims were ticketed for the event and that 70 bishops, mostly from Eastern Europe, would join in. Benedict called the anniversary "the reason for my coming" and said he would go as a simple pilgrim.
Benedict's visit concludes Sunday with a Mass at Vienna's St. Stephen's Cathedral and a visit to the Heiligenkreuz abbey outside the capital.
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