What is 'normal'?
Is normal an innate quality, or does society set the terms for what is normal? Dysart has dedicated his career to giving children 'normal' lives, and he attempts the same for Alan in this play; however, treating Alan exacerbates his doubts about the purpose of his career. Equus argues that normal is not always ideal, and that madness is constructed by society.
Religion
Horses are Alan's personal religion. He worships Equus as his god, equating him to Jesus and insisting that he wears chains to pay for humanity's sins. This unique religion is what gives Alan his sense of self, and Dysart says that to take away a person's worship is the worst thing someone could possibly do. Dysart himself wishes he could feel such a strong religious calling, and he is fascinated by the Ancient Greeks, who saw small, individual gods in everything. In many ways, Equus provides examples of unconventional means of worship that are just as important as mainstream religions.
Sexuality
As a seventeen-year-old, Alan is attempting to balance his budding sexual desires with his strong will to please his god, Equus. He describes his moments with horses with sexual excitement, which sets up an intimacy between the two that make it all the more blasphemous when he attempts to sleep with Jill. Jill serves as a test for Alan to see if he can channel his sexuality down a normal path, but in the end, he fails.
Pain
Hesther Salomon's main argument behind wanting Dysart to continue treating Alan is that the boy is in pain, and that Dysart can take this pain away. By Dysart argues that the cause of this pain might not be entirely unwanted, which sets up another major theme of the play. Removing this pain comes with a price, as this pain is a product of Alan's extreme passion. To remove the pain would be to remove the passion as well, and without this passion, Alan would have very little left of himself. Dysart is even jealous of Alan's pain, since he feels that he has none of this kind of passion in his dull life.
Blame
Aside from fixing mental illness, a psychiatrist's primary job is to figure out the origins of mental illnesses. Before he can truly treat Alan, Dysart must dig deep into his childhood to find the root cause of the crime he committed; naturally, he looks towards his family and home life. This raises the question of who is truly at fault for Allan's actions: Alan's parents for the way they raised him, or Alan himself.
Freedom
One of the first things Alan notices about horses is the chains that bind them. He is fixated on the bits in their mouths and the reins around their necks, seeing these as despicable means of confinement and constriction. This is primarily because Alan himself feels confined by the life he lives and the expectations of his parents and of society, when truly all he wants is a sense of freedom. Alan achieves this freedom through his midnight field rides on Nugget's back, with both horse and rider completely naked and free of the ties that bind them -- a freedom which he conflates with the sexual act.
Duty vs. Morality
Dysart's entire career is a constant struggle between doing his duty and upholding his personal convictions. It is clear throughout the course of the play that he does not truly believe that something is inherently wrong with Alan; however, his duty is to relieve this child from pain and make him 'normal' again. Dysart endures many moments of uncertainty about how correct his duty really is. In particular, the dream he has about sacrificing children represents these doubts in an incredibly haunting way.