Yad Vashem chair Avner Shalev is guiding Prince William through the memorial's exhibitions detailing the death of six million Jews systematically killed by Nazi Germany and its collaborators during World War II.
"Terrifying. (I'm) trying to comprehend the scale", the Duke said.
He said: "Today's visit to Yad Vashem was profoundly moving and deeply inspiring".
Today, William will travel to Jerusalem, a history-making move denoting the first time a member of the British royal family has visited Israel on the government's behalf.
At the residence, the prince met relatives of the late Rachel Cohen, who was hidden from the Gestapo, along with two of her five children, by Princess Alice, the mother of Britain's 97-year-old Prince Philip, in her palace in Greece. "We know some of the politics are hard, but this is not a political visit".
On Thursday, Prince William is to complete his stay by visiting historical and religious sites in Jerusalem. The princess died in 1969, and in 1988 her remains were brought to Jerusalem.
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A devoted Aston Villa fan, William, 36, is wearing beige trousers and a tie-less sky blue shirt, while 23-year-old Hussein, is wearing a short-sleeved T-shirt and jeans. While here, the future king was scheduled to make high-profile stops at major sites across the country, including Yad Vashem, Jerusalem's Old City and the Western Wall, as well as meetings with Israeli and Palestinian leaders.
The visit to Jerash came on the second day of a five-day tour that also takes William to Israel and the occupied Palestinian territories.
Prior to watching England thrash their South American rivals 6-1 on Sunday evening, William spoke at a garden reception at the British Embassy, praising Britain's historic ties with Jordan and the kingdom's commitment to hosting Syrian and Palestinian refugees.
Later Monday, he'll be the first British royal to visit the Holy Land in an official capacity.
"It is nearly impossible to comprehend this appalling event in history". "I'm very much looking forward to really absorbing and understanding the different issues".
At a meeting with Israeli President Reuven Rivlin, the prince, on a visit described by Britain as non-political, said he hoped "peace in the area can be achieved".
Prince William attended a football game between young Jewish and Arab players in Tel Aviv, Israel.