The 11 imams, sheiks and religious teachers from nine countries met a Holocaust survivor and Poles whose families risked execution to save Jews from the Nazis, in the Polish capital's Nozyk Synagogue as part of the tour.
They have been around museums, including the recently opened Museum of the History of Polish Jews on the site of the former Jewish Ghetto in Warsaw. And they also visited the Auschwitz and Dachau concentration camps.
"The main aim is to get Muslims who are leaders all over the world, particularly in the Middle East, to acknowledge the reality of what happened here and to be able to teach it to the people that they lead," said trip organiser Rabbi Jack Bemporad, who is executive director of the US-based Center for Interreligious Understanding.
He was standing underneath the red brick watchtower over the main entrance to Birkenau, the largest of more than 40 camps that made up the Auschwitz complex. This was where the Nazis installed four gas chambers and crematoria to speed up the murder and disposal of people, who were mostly Jews, from across Europe.
Auschwitz-Birkenau, set up by the Germans in Nazi-occupied Poland, is largely intact and is now a museum. Historians estimate 1.1 million people were killed there - one million of them were Jews but there were also Poles, Roma, Soviet prisoners of war and others.
"I think that when someone wants to deny the Holocaust or think that it is exaggerated, which many of them do and certainly many of their followers do, when they come here and see it, their experience is such that they can no longer think that," Rabbi Bemporad said.
Beside the ruins of one of the gas chambers - the Germans blew them up as they retreated, in an effort to hide their crimes - the Muslim leaders paused for a moment's silence.
"You may read every book about the Holocaust but it's nothing like when you see this place where people were burned," said Mohamed Magid, president of the Islamic Society of North America.
"This is the building, the bricks. If they were to speak to you and I, they would tell you how many cries and screams they have heard."
Mr Magid, who is originally from Sudan, first visited Auschwitz-Birkenau during a trip organised for American imams in 2010. He said the experience had led him to hold an annual Seder, a Jewish ceremonial meal, at his mosque in Virginia where he invites people to listen to the story of a Holocaust survivor who was saved by a Muslim family.
"We go back more committed to human rights and more understanding of conflicts and how to resolve them, but also to be careful of a curriculum that teaches racism and hatred," he said.
Earlier, the group had taken photos as they walked around an exhibition in the red brick barrack blocks at Auschwitz, about 2 miles (3kms) from Birkenau.
They made comments such as "Can you imagine?" and "It's beyond comprehension" as they saw a great pile of hair shorn from women prisoners that was used to make rudimentary textiles. They shook their heads as they saw faded children's shoes and dolls in glass cases.
After they had seen just two of the 14 exhibition blocks, some of the group asked for a break and they knelt in prayer beside the camp's execution wall.
Barakat Hasan, a Palestinian imam and director of the Center for Studies and Islamic Media in Jerusalem, said he "didn't know many details about the Holocaust" before the trip.
"I felt my heart bleeding when I was looking at all this. I was fighting back tears," he said through an interpreter. "As a Palestinian living under occupation, I feel sympathy for the pain and injustice that was inflicted on the Jews," he added.
Mr Hasan said he did not believe there were people in the Muslim world who denied the Holocaust happened, but he said there was discussion in his community about whether the commonly quoted figure of six million Jewish victims was correct.
"Maybe now after seeing what I've seen, maybe the numbers are correct also," he said, adding that he would write articles and mention his trip on Facebook.
As he walked along the railway line and unloading ramp at Birkenau - where the trains hauling cattle cars crammed with Jews arrived - Ahmet Muharrem Atlig, a Turkish imam and secretary general of the Journalists and Writers Foundation in Istanbul, said he wept when he saw a photograph that showed children looking scared as they got off a train.
"Unfortunately the Muslim communities and congregation don't know much about the Holocaust," he said.
"Yes, we've heard something. But we have to come and see what happened here. It's not just about Jews, or Christians, this is all about human beings because the human race suffered here."
Muslim leaders from around the world have taken part in an unprecedented trip to Germany and Poland to see and hear for themselves about the horrors of the Jewish Holocaust.