The museum's most talked-about exhibit is "The Holocaust Section", where visitors are divided into groups to take their own place in some of the events of World War II.

In addition, the museum features a "Tolerancenter" that discusses issues of prejudice in everyday life, a Multimedia Learning Center, Finding Our Families – Finding Ourselves, a collection of archives and documents, various temporary exhibits such as Los Angeles visual artist Bill Cormalis Jr's "'A' Game In The B Leagues", which documents through paintings, the Civil Rights Movement during the segregation of colored people in Major League Baseball, and an Arts and Lectures Program.

A classroom visit to the museum is featured in the 2007 movie Freedom Writers, based on the real-life story of high school teacher Erin Gruwell and her students.

[7] In 2003, Christopher Reynolds wrote, for the Los Angeles Times, that the museum lacked any exhibit about the Armenian genocide.

[8] Political theorist Wendy Brown critiqued the museum in a chapter of her 2009 book Regulating Aversion: Tolerance in the Age of Identity and Empire; in the book, Brown analyzed "tolerance as a museum object", and made connections between the Israeli–Palestinian conflict and genocide directed at non-Jewish groups.