Transformation
Hartman tells the men that his primary goal is to turn them into "killers," and the entire boot camp sequence is essentially a crucible in which the men must leave their humanity behind and become unthinking destroyers. Joker says in voice-over, "The Marine Corps does not want robots. The Marine Corps wants killers." Drill Seargent Hartman uses any details he gathers about the men to humiliate them, such as when he mocks Cowboy, encouraging them to make a clean break from their former lives. Giving the men nicknames also reinforces the fact that their identities undergo a profound shift in basic training and thereafter. Whether or not this transformation is ethically defensible—whether it makes them survivors, or merely monsters—is one of the film's central moral questions. Joker seems to cautiously endorse the process, saying at the end of the film, that he's "alive" and "no longer afraid."
Masculinity
Masculinity is at the heart of Kubrick's film; only three women appear in the entire story. The "boot camp" sequence is entirely male, demonstrating the kind of extreme psychological harm and physical debility that men in particular are expected to withstand and inflict on each other in the military. Hartman only invokes femininity to mock the men, such as constantly referring to them as "ladies." Hartman also attempts to humiliate their manhood in other ways, such as when he calls Cowboy a "queer," or when he makes Pyle march with his pants around his ankles while sucking his thumb. Manhood and masculinity are the horizons toward which all the men aspire, as evidenced by Joker constantly lapsing into his John Wayne impression. Only Joker seems to understand the futility and absurdity of performative masculinity, as opposed to a character like Animal Mother, who takes his own authority deadly seriously.
Waste
Waste is a central theme of the film, one that manifests itself in a number of ways. Hartman constantly refers to the men as "shit," and threatens to "shit down the neck," of one of the recruits. Kubrick films Joker and Cowboy mopping the latrines when discussing Pyle's mental fitness, and Pyle is sitting on a toilet before he kills Hartman and himself. The men routinely use the word "wasted" to refer to men killed in combat. Joker asks where "the shit" is upon arriving in Phu Bai, so that he can find action to report on in his correspondence. Through the theme of waste, Kubrick conveys how war literally turns men into refuse, as evidenced by the shot of Joker looking down into the mass grave of Vietnamese corpses covered in lye.
Sexuality
Despite Hartman's declarations that the men must leave all sexual fantasies behind upon entering boot camp, sexuality nevertheless persists as a major theme of the film, becoming perversely entangled with the sadism and violence of war. The scene where the men grab their crotches and hold their rifles, chanting, "This is my rifle! This is my gun! This is for fighting! This is for fun!" makes an explicit connection between male genitalia and weapons of war. The boot camp sequence is inevitably homoerotic, given that all of the men are sleeping, showering, and living in close quarters together, with virtually no privacy. Hartman encourages the men to form a quasi-sexual relationship with their rifles by giving it a woman's name. Cowboy describes how a Marine named Handjob was so desperate for sexual relief that he began compulsively masturbating until a Navy psychologist deemed him a "Section 8." In Full Metal Jacket, male sexuality has become completely warped by the process of war.
Duality
When a colonel interrogates Joker about why he wears a peace symbol as well as the inscription "BORN TO KILL" on his helmet, Joker replies, "The duality of man. The Jungian thing, sir." The Jungian notion of duality heavily influenced the way Herr and Kubrick adapted Hasford's novel on-screen, as both were interested in exploring the "shadowy" side of humanity that war exposes. Pyle, for instance, is arguably the kindest and most sensitive recruit in boot camp, until the abuse inflicted upon him by Hartman and the platoon transforms him into an unstoppable killing machine. Kubrick's diametrically opposed shot-reverse shot patterns also visually figure the notion of duality, providing two opposite perspectives of an identical scene, place, or object. Animal Mother, both masculine and feminine, a protector and a destroyer, is another example of duality.
Representation
Kubrick's film purposefully asks whether war can ever be faithfully captured, whether in print, with images, or on film. Joker's job as a combat correspondent includes daily briefings where Lockhart, Joker's editor-in-chief, officiously redacts certain phrases from use, and pressures the writers to produce stories that are flattering to the war effort. Propaganda, not reality, is what combat journalists are trained to generate, something that Kubrick's collaborator Michael Herr also explored in his Vietnam war memoir Dispatches. When the news crew interviews the Lusthog Squad, they affect different demeanors, such as Animal Mother, who is subdued, and Cowboy, who halts and stumbles over his words. Given that the men behave differently on camera, Kubrick conveys how the very nature of war itself seems to resist representation and documentation.
Insanity
Full Metal Jacket demonstrates the range of mental deterioration that can happen to men who are trained to do one thing only: kill. Although each man reacts to the challenges of war in a different way, no man emerges unscathed from the horrors they are forced to endure. The ritual humiliations of boot camp drive Pyle insane early on, leading him to talk to his rifle and murder Hartman. Crazy Earl, implicated in madness by his very name, props up a Vietnamese corpse and pretends it's his "bro." Animal Mother is liable to volatile, uncontrollable bursts of aggression. Crazy Earl, Animal Mother, and the helicopter gunner all try to stave off madness by taking sheer, animal pleasure in killing. Handjob compulsively masturbates until he is deemed clinically insane. Kubrick conveys how war has a corrosive effect on every man's mental stability.