Pain
Both physical and psychological pain are central themes in the novel, and Yanagihara also explores how these two different types of pain intersect with one another. After his traumatic childhood and adolescence, Jude is left with injuries and diseases that will cause him to experience physical pain every day for the rest of his life. His condition will never improve, deteriorating over the course of his life. In addition to his physical pain, Jude is also tormented by traumatic memories, flashbacks, and a constant sense of doom and foreboding. In order to cope with the pain he carries, Jude chooses to inflict more pain on himself by engaging in increasingly gruesome acts of self-harm. Jude finds solace in the pain he inflicts because he can control it and because it gives him a more acute sensation to focus on. Pain is a key component of Jude's experience because it makes him isolated and fundamentally different from other people. No one can ever truly understand Jude because he hides much of his physical and emotional pain from them.
Friendship
During their college years, Jude, Willem, Malcolm, and JB form a close friendship that endures over the rest of their life. Jude subsequently goes on to make other friends, such as Richard, Lucien, and (in some ways) Andy, who also enrich his life and become sources of support. Jude and Willem's friendship ends up revealing that they are the loves of one another's lives, although their partnership ends up being a hybrid of friendship and romance. For all four men, the centrality of friendship in their lives is striking and sometimes gives them pause. Many people around them note that, as they grow older, it would be expected for them to pair off, marry, and possibly have children. Malcolm is the only person who enters into a long-term relationship, and he and his wife never have children. As for the others, they realize as they age that friendship is the bond they most want to have at the heart of their lives. Because of the long-enduring friendships, the group always has a connection to their past and a sense of continuity.
Secrecy
Secrecy is a central theme in the novel because Jude hides most of the details of his past even from his closest circle, including Harold and his friends. When Jude meets the rest of his friend circle in college, he is extremely vague about his past, his family, and any possibility that he might have a romantic life. Even after he has known his friends for decades, he does not disclose any of this information. After he becomes close with Harold and Julia, Jude also keeps many secrets from them. It is not until after Jude dies by suicide in his fifties that Harold learns the full truth of all the abuse and trauma Jude suffered as a child. In addition to his past, Jude is also secretive about his self-harming because he knows that Willem, Harold, and others would try to stop him. Jude's secrecy causes tensions in his relationships because it forces people like Andy to keep secrets on his behalf, and it almost drives Willem away. Still, even though he can see that his secrecy is destructive, Jude cannot let his guard down and trust in the unconditional love of his family and friends.
Sexuality
Sexuality is an ambiguous concept for many of the characters, as the four friends seem to have flexible sexual identities. They experience attraction on the basis of their connection to others, not on the basis of any particular gender identity. When Willem realizes he has romantic feelings for Jude, it is natural for him to want to have sex with him, even though he hasn't previously pursued relationships with men. The novel shows that while sexuality can be fluid and evolving, it can also be fixed. Because of Jude's experiences with sexual trauma at a young age, he is never able to experience sexual pleasure or reclaim his sexuality. Even though many people try to persuade Jude that he deserves to be able to enjoy his sexuality, he is too scarred by his past experiences to be able to experience pleasure even with someone he loves and trusts completely.
Success
Jude and his three closest friends all experience extreme success in their respective careers. Malcolm, JB, and Willem initially experience doubts and impatience about the creative career paths they choose, but they end up famous and wealthy in their fields. Jude is more strategic about building a lucrative career path, but he also ends up excelling at the work he does and becoming extremely successful as a lawyer. However, the novel uses the theme of success to show that fame and money guarantee neither happiness nor safety. No matter how much success the characters experience, Malcolm and Willem still lose their lives to tragic and unexpected deaths. For Jude, the lack of connection between success and happiness is even clearer. No matter how much money and prestige he accumulates, he continues to feel haunted and ashamed.
Family
Throughout the novel, family is often a source of confusion and tension. When the four friends meet in college, Willem and Jude feel an affinity for one another because they are both orphans. In contrast, Malcolm and JB have the ongoing presence and support of loving families. Malcolm and JB sometimes feel frustrated because of the dynamics within these families, but they undoubtedly benefit from the support and sense of identity they have. Through incredibly good fortune, Jude ends up being adopted by Harold and Julia, giving him an unexpected chance at having a family who loves him unconditionally. Through the bonds Jude forms with his college friends (especially Willem), Harold, and Julia, the novel shows that families can be chosen and made. They do not simply have to be biological units that someone is born into.
Disability
The incident in which Dr. Traylor hits Jude with his car leaves Jude not only with pain but also with impaired mobility. His ability to move around independently degrades as he ages and his symptoms worsen. Throughout the novel, the theme of disability is used to illustrate how Jude's early traumas impacted his life. His disability functions as a metaphor for how he has been psychologically and emotionally impacted by his early life. Many people take the ability to walk around for granted, but for Jude, this is a challenging and painful process. In the same way, building relationships, falling in love, and trusting people are extremely hard for Jude even though they come easily to others. Jude is extremely sensitive about his disability because he fears it will cause people to see him as weak or vulnerable. For example, Jude is never able to forgive JB because JB mocks Jude's limp, thereby confirming Jude's deepest fear about how people perceive him.