His words were seen as the crowning chapter to efforts throughout his 22-year papacy to reconcile Jews and Christian. Still, many Jews had hoped for more.
The pope did not assign any blame to the Catholic Church hierarchy, and he did not mention Pope Pius XII, the wartime pontiff accused by many Jews of staying silent while their people were killed.
In a ceremony at the dark, candlelit Hall of Remembrance at the Yad Vashem Holocaust Memorial, its stone floor engraved with the names of death camps, the pontiff laid a wreath in memory of the six million Jews who perished in the Nazi genocide - among them childhood friends from the small Polish town of Wadowice.
"As bishop of Rome and successor of the Apostle Peter, I assure the Jewish people that the Catholic Church, motivated by the Gospel law of truth and love, and by no political considerations, is deeply saddened by the hatred, acts of persecution and displays of anti-Semitism directed against the Jews by Christians at any time and in any place," the pope said.
The visit capped a morning of remarkable gestures to Israel and the Jewish people.
In a meeting with President Ezer Weizman, the pontiff blessed Israel, an act seen by many Israelis as final church recognition of their state. For centuries, the Catholic Church taught that the Jews' exile was punishment for the death of Jesus.
In sharp contrast, Pope Paul VI, the last pontiff to visit the Holy Land in 1964, had not mentioned Israel by name and refused to address the Israeli president at the time, Zalman Shazar, by his title.
In a display of Catholic-Jewish amity, the pope also met Israel's
two chief rabbis, Eliyahu Bakshi Doron and Israel Meir Lau, at their office
in west Jerusalem. The two black-robed, bearded rabbis handed the white-clad
pontiff a Bible, the dedication an allusion to religious co-existence, taken
from the book of the Prophet Micah. "For all the people who will walk, everyone
in the name of his God, and we will walk in the name of the Lord, or God, forever
and ever."