Author's Saving Throw: A fair amount of historical inaccuracies in the book were fixed in the movie. For instance, in the book the fence wasn't electrified and Bruno could easily pull up a loose part of it. In the film, it is electrified, as shown when he throws a rock at it, and he has to be very careful crawling under it instead. Several of the more implausible plot points like Bruno not knowing who Adolf Hitler is are also omitted.
Crowning Moment of Heartwarming: ...Despite the mayhem that followed, Bruno found that he was still holding Shmuel's hand in his own and nothing in the world would have persuaded him to let go. Also a Tear Jerker.
Nightmare Fuel: Parents will not have pleasant dreams for quite a while after this.
The music that plays during the climax of the film version is absolutely terrifying, if only just to hammer in just how horrifying and tense the event at hand is.
The final shot of the movie, which is a panning-away shot of the gas chamber Bruno and Shmuel died in. The chamber is completely silent.
Some Anvils Need to Be Dropped: The setup of the two boys meeting at the fence and the contrivance of Bruno being able to dig under the fence can be nit-picked for historical veracity and plausibility, but the story very effectively highlights the evil of locking up and exterminating people because of their race and/or religious background, as well as the danger of indoctrinating impressionable children about the supposed 'evils' of other groups. While the ending may not have ever happened to any SS Officer and his family in real life it does make the point that people who do evil may find their actions rebounding on them in major and unexpected ways.
Captain Obvious Aesop: Don't discriminate people based on what they're born with! ...sadly enough, the above trope still holds true in the present day.
What Do You Mean, It's Not for Kids?: Yes, it's a story about two boys from vastly different backgrounds overcoming their differences and becoming true friends... but it's still about the Holocaust. Generally, it's often placed in middle school libraries.