The relationship between the two boys is the heart and soul of Boyne's novel, set in Nazi Germany.
Bruno is nine-years-old. He has just moved from is home in Berlin to a new, unfamiliar place called "Out-With" (Auschwitz). Although he longs to explore his new environment, Bruno has been warned, sternly and repeatedly, that certain areas around his home are forbidden. Despite these admonitions, however, one day Bruno's curiosity gets the best of him and he sets off to investigate.
As he wanders, Bruno comes upon a fence. On the other side of the fence is a boy who seems to be about Bruno's age. This boy, of course, is Shmuel. Shmuel wears what appear to be striped pajamas. He sports a cloth cap. Bruno notices that the boy is barefoot. The boys strike up a conversation. They discover they share the same birthday, April 15th, 1934. Bruno observes that there are many other people on Shmuel's side of the fence but he does not know what they are doing there.
Bruno continues to sneak out and meet Shmuel at the fence. Bruno has learned, although he is mystified why, that he and Shmuel are supposed to be enemies. He tells Shmuel as much:
"We're not supposed to be friends, you and me. We're meant to be enemies. Did you know that? ”
The boys, innocent of the political machinations of their elders, do not care about "not supposed to be." They are friends. As they continue to meet and talk, their bond becomes stronger and stronger. Shmuel expresses his fear about his missing father; Bruno promises to see if he can find anything out.
Shmuel is happy to accept Bruno's offer of help. He tells his friend that he will acquire another set of striped pajamas so that Bruno can blend in and look for Shmuel's father with less risk of being stopped and questioned.
The ruse works too well. The prisoners are unexpectedly herded into a gas chamber, Bruno among them. The friends die, holding hands. Bruno's earlier words were completely true: "You're my best friend, Shmuel," he said. "My best friend for life.” Sadly, both of their lives are horrifically short.