Although protagonist Charlie Gordon is an adult, Flowers for Algernon is a coming-of-age story with which both children and adults readily identify. As his intelligence increases, he must confront emotional, social, and ethical issues previously beyond his understanding. As he regresses, he faces loss with dignity and determination.

As critic Robert Small, Jr., points out, the question “What if I were smarter?” occurs to all children and adolescents, especially in the competitive school environment. Daniel Keyes answers that question well, in a complicated but not a confusing manner, showing the benefits and pitfalls of genius.

Many critics have praised the novel for its treatment of the mentally handicapped. Keyes’s depiction is emotionally powerful but flawed; for example, Charlie’s sexual desire fully awakens only after the operation (he is surprised by his first nocturnal emission), although in reality mental retardation does not prevent sexual maturity. Nevertheless, that awakening may contribute to Charlie’s appeal among young adult readers, and the novel’s plea for empathy is obvious and convincing. The most accurate depiction of mental illness can be found when Charlie visits the Warren State Home, a scene that seems to be based on an actual visit to the institution.

Although the reader identifies with Charlie emotionally, other characters present conflicting views, enriching the novel. When Charlie and Alice debate human nature, both make good points; the bakery coworkers are shown both harassing Charlie and befriending him, a realistically paradoxical mix.

Some critics argue that, for science fiction, Flowers for Algernon contains little fictional science. Actually, the process is described in some detail, including surgery, enzyme treatments, and subliminal teaching during sleep, although the emphasis is on the resulting changes in Charlie. Much speculation in the novel concerns Freudian psychology, with Keyes examining such issues as the importance of the unconscious, the remembrance of past traumas to cure current problems, and the dangers of a sexually repressive upbringing.

Critic Paul Williams sees stories about increased intelligence, such as Flowers for Algernon and Poul Anderson’s Brain Wave (1954), as a modern myth, perhaps condensing the past centuries of human scientific development to an individual scale. If so, he points out, Charlie’s return to his prior state, or worse, may show modern society’s insecurity about technology and anxiety about the state that would result should it be lost.