In The Boy in the Striped Pajamas, it is prejudice against the Jews which manifests itself in outright discrimination when the Jews are rounded up and sent to camps like "Out-With" (Bruno's mispronunciation) in trains with no doors such as Shmuel describes. Bruno is skeptical of what Shmuel says because it sounds so far fetched to him, especially when there was plenty of room in the carriages his family traveled to Poland in.
Bruno's father reveals the extent of the problem when he tells Bruno " they're not people at all, Bruno...Well, at least not as we understand the term" (chapter 5) after Bruno inquires about the people in the curious striped pajamas that he has seen from his window. Bruno also witnesses Lieutenant Kotler's inhumane treatment of Pavel when he overhears him speaking to Pavel in a most disrespectful way. Bruno thinks that there is "something about the harsh sound of it" which embarrasses him and makes him "feel ashamed" (chapter 7).
The issue of prejudice will resolve itself most tragically when Bruno borrows a pair of striped pajamas and goes under the fence to join Shmuel. Even Shmuel is most surprised at the boys' likeness once they are both in pajamas. Only the fact that Bruno is "nowhere near as skinny" prevents the boys from being "almost (Shmuel thought) ...all exactly the same" (chapter 19). There is now no difference between them which shows that the prejudice shown by the Nazis is surface deep and has no foundation.
As the story takes place with the Nazi regime in power, prejudice against Jews is a fervent theme throughout the novel. However, since the protagonist Bruno is a young boy, he does not fully understand it. Despite having a father employed by the Third Reich, a tutor who pushes an agenda of antisemitism and a sister that prominently adopts Nazi ideology, Bruno does not embrace hate or judgment against people different from him. Instead, he longs for companionship and is fond of anyone that shows him kindness. As he meets a boy his age that lives behind a fence, he cannot fathom the boy's stories of little food and danger. His new friend is his only confidante. This relationship shows that prejudice is not inherent and even when a child is being indoctrinated, they cannot "fathom" the evil that results from extreme discrimination.