Bells tolled and incense filled the air as worshippers returned to the Church of Nativity for the first services since the end of a five-week standoff between Israeli troops and Palestinian gunmen.

Nearly 1,000 people, far more than usual, gathered for Greek Orthodox and Catholic services Sunday at the 4th-century church, one of Christianity's holiest sites.

As they entered, each made the sign of the cross and reviewed damage from the standoff between Israeli soldiers and Palestinian gunmen. Some stopped to gaze at the bullet holes that scarred the outside walls.

Candles burned at the entrance to Jesus' birth grotto and those who visited the area knelt and kissed the star believed to mark the spot where Christ was born.

"We are happy to be here, to attend the services after a long absence," said Alberta Katan, 65. "When I entered, I felt joy in the eyes of the people praying again in the basilica."

For 39 days, the church was home to scores of Palestinian gunmen and civilians. By the time the ordeal ended, the place reeked of urine and was filled with garbage, dirty dishes and cigarette butts.

But volunteers spent Saturday furiously cleaning, and by the time services started Sunday the church smelled pleasantly of incense. All that remained of the mess were some mattresses and blankets that children played with in the courtyard.

"We have to bring peace to Jesus' land by dialogue and justice and not by violence," said Cardinal Roger Etchegaray, a Vatican envoy involved in ending the standoff, told worshippers.

In a separate service, Christian residents from Bethlehem sang hymns as the Greek Orthodox patriarch Irineos I led prayers.

After the services, Palestinian flags were raised above the compound next to the church while banners in English and Arabic were draped over the building. One declared: "The Nativity Church believes in peace and justice."

Israeli forces, who had entered the West Bank as part of an operation to root out Palestinian militants, encircled the church April 2 when Palestinian gunmen fled inside.

The standoff ended Friday with the agreement to deport 13 Palestinian militants to Europe and to send another 26 to Gaza. Soon after the Palestinians left the church, the Israeli army pulled out of Bethlehem, the last Palestinian city it still occupied.

At the Vatican, Pope John Paul II said he was relieved.

"From my heart I thank all those who contributed to restoring to the holy place its true religious identity," John Paul said. "A special mention goes to the communities of Franciscans, Greek and Armenian Orthodox who, with notable sacrifice, remained faithful to the sanctuary."

The pontiff said Bethlehem could serve as inspiration in the search for peace between Israelis and Palestinians.

"Bethlehem's universal message is love, justice, reconciliation and peace," the pope said. "And it is on these bases that one can construct a future respectful of the rights of the Israeli and the Palestinian peoples, in mutual trust."

During the siege, the bells continued to ring Sunday mornings even after one of the bell ringers was shot dead during the confrontation. This Sunday, the pealing of the bells signaled a return to normalcy.

Father Ibrahim Faltas, 38, a Franciscan in charge of the shrine, recalled a dangerous moment.

One day he got up in the morning and opened the window in his room, making some noise, he told The Associated Press. "(Israeli) soldiers had taken positions under my window and they opened fire," he said. "The bullets passed very near to me.

The Israeli military had no immediate comment about the incident.

When the gunmen left, he said, "their last words to all the priests and monks were, 'thanks, Father, and we are sorry for everything that has happened."'