John Boyne uses a series of techniques to explore the themes of discrimination and prejudice in The Boy in the Striped Pyjamas.

First, he writes the story through the eyes of Bruno, a pretty normal German boy, whose father is an SS Officer. Through doing this, Boyne is able to present the Holocaust through a set of innocent eyes, almost blind to the indoctrination and ideologies that underpinned the Holocaust shared by adults. Bruno finds it difficult to understand why certain people (Jews) are treated badly. The book goes further by exploring this discrimination through the friendship Bruno forms with Schmuel, the Jewish boy in the Death Camp. He has no understanding why this friendship should be forbidden, but knows that society is telling them that they should be enemies.

Another way the book explores the themes of prejudice and discrimination is by presenting a range of Nazi characters from particularly harsh ones (like Lt. Kotler) to Bruno's father who is portrayed as a kinder man just doing his duty. What the author does here is 'normalize' the horror of the Holocaust. This is an important idea because we think of the Nazis as murderous monsters who carried out these horrific acts. While all that is true, we tend to forget how normal many of these people probably appeared. They had dinners together, talked about life and music. While at the same time, they were murdering millions of people that they considered 'less human.'

Boyne's novel clearly suggests that the Holocaust was the result of prejudice and discrimination.  Boyne does not take a complex path to this.  He asserts that if more individuals viewed reality as Bruno did, the Holocaust and events like it would cease to exist.  This becomes clear in the Author's Note:  

. . .only the victims and survivors can truly comprehend the awfulness of that time and place; the rest of us live on the other side of the fence, staring through from our own comfortable place, trying in our own clumsy ways to make sense of it all.

Boyne's way that seeks to "make sense of it all" suggests that when individuals shed "staring" at one another through "the fence" that is built through prejudice and discrimination, events such as the Holocaust do not need to happen.

It is a foundational premise, but one that Boyne reminds the reader of continually in the text.  These reminders are seen in the private realm and in the public domain.  When Bruno admonishes Gretel for treating Maria as merely a servant, it is reflective of how Bruno stands against prejudice and discrimination.  Bruno detests Lieutenant Kotler in part because of his savage treatment of Pavel and Shmuel, representative of prejudice and discrimination.  A large component of why Bruno and Shmuel get along so well is that they see one another as brothers, individuals who are not separated by the condition of prejudice and discrimination.   Boyne wishes Bruno's example to be modeled for all, as "nothing in the world" gets in the way of Bruno telling Shmuel that there is a lifelong friendship between them.  Prejudice and discrimination are elements that human beings can withstand if they view individuals as ends in their own right.  As Bruno walks with Shmuel to both of their deaths, it becomes clear that Bruno is willing to stand against these qualities until the very end.  Boyne makes clear that the prejudice and discrimination are viewed as the root causes of the Holocaust.  If individuals stand against these forces as Bruno did, there is a greater chance of stopping such atrocities.