Innocence is an important theme throughout the novel. Although Bruno and Shmuel share a certain childlike innocence, the reality is that Shmuel is a prisoner in Auschwitz and has certainly seen horrific sights. Bruno, on the other hand, is fiercely protected by his parents who do not want him to know about the horrors of the reality that is the Holocaust; in particular, they go to great lengths to keep the details of Bruno's father's job a secret from him. The juxtaposition of such innocence with the inherent evil of the Holocaust sets a poignant tone. This theme reinforces the idea that hatred and prejudice are learned behaviors.
Another significant theme in the novel is friendship. The desire for friendship is universal and at no time is it more important than during childhood. Bruno and Shmuel exist in two completely different worlds but share a mutual desire for companionship during a difficult and lonely time. In spite of their remarkably different circumstances, Bruno and Shmuel forge a meaningful friendship. As their friendship develops, it is tested on many occasions as the boys navigate their individual realities. When Shmuel is brought to Bruno's house to work as a servant, Bruno denies knowing him and giving him food; consequently, Shmuel is punished for stealing food (which Bruno had given him). Both boys know that they would be in terrible trouble if anyone were to find out about their friendship so they keep it a secret. Ultimately, the boys unknowingly march to their death hand in hand with no one in the world but each other.
The theme of human nature also proves to be central to the story. Readers will question how Bruno's father and sister, along with so many other Germans, can be such staunch believers in the Nazi propaganda while Bruno remains compassionate and even, some might argue, resistant to the same ideas. Bruno and Shmuel represent all that is kind and decent in humans as well as the potential that they have to do good. Conversely, Bruno's father and Lieutenant Kotler reveal man's capacity for evil. The novel points out the choice humans must make regarding how they treat others. On a similar note, The Boy in the Striped Pajamas also considers the dangers of conformity and people's reluctance to take a stand in the face of adversity.