There is an overriding feeling of loss after having read The Boy in the Striped Pajamas as two innocent boys with such diverse futures ahead of them, suffer the same fate. Boundaries based on race, creed or any other form of discrimination have no part in the lives of children and there is a warning contained in the story's moral that adults who attempt to create an environment of inequality may be the ones who suffer the most from their own prejudices.
Power is a tool that can be used to do good but which can also be self-serving and corrupt. Anyone in a position of power can learn from this story. Bruno's father uses his power to destroy lives but Bruno uses his power - in this case his freedom - to help Shmuel, even minimally.
The innocence of the boys also teaches the reader that friendships form in unlikely circumstances and are not based on having similar backgrounds, similar education or moving in the same circles. Friendships are often formed out of necessity and a need to connect and interact thus revealing a common goal - regardless of circumstances or background. Everyone seeks acceptance.
Bruno and Shmuel become friends because they are unaware of the prejudices of the people around them. The boys are aware of the soldiers' cruelty but the reasons for it escape them. This teaches the reader that prejudices are the domain of society and are a creation of society. They are not real differences but perceived ones.
The ultimate irony is the fact that the boys share a birthday and so even their parents would have something in common. In another world, they may have attended the same birthday party!