Regarding her emphasis of the grotesque, O'Connor said: "anything that comes out of the South is going to be called grotesque by the northern reader, unless it is grotesque, in which case it is going to be called realistic." Her texts usually take place in the South and revolve around morally flawed characters, frequently interacting with people with disabilities or disabled themselves (as O'Connor was), while the issue of race often appears in the background. Most of her works feature disturbing elements, though she did not like to be characterized as cynical. "I am mighty tired of reading reviews that call A Good Man brutal and sarcastic," she wrote. "The stories are hard but they are hard because there is nothing harder or less sentimental than Christian realism. ...When I see these stories described as horror stories I am always amused because the reviewer always has hold of the wrong horror."
She felt deeply informed by the sacramental and by the Thomist notion that the created world is charged with God. Yet she would not write apologetic fiction of the kind prevalent in the Catholic literature of the time, explaining that a writer's meaning must be evident in his or her fiction without didacticism. She wrote ironic, subtly allegorical fiction about deceptively backward Southern characters, usually fundamentalist Protestants, who undergo transformations of character that, to her thinking, brought them closer to the Catholic mind. The transformation is often accomplished through pain, violence, and ludicrous behavior in the pursuit of the holy. However grotesque the setting, she tried to portray her characters as open to the touch of divine grace. This ruled out a sentimental understanding of the stories' violence, as of her own illness. She wrote: "Grace changes us and the change is painful."
She also had a deeply sardonic sense of humor, often based in the disparity between her characters' limited perceptions and the awesome fate awaiting them. Another source of humor is frequently found in the attempt of well-meaning liberals to cope with the rural South on their own terms. O'Connor used such characters' inability to come to terms with disability, race, poverty, and fundamentalism, other than in sentimental illusions, as an example of the failure of the secular world in the twentieth century.
However, in several stories O'Connor explored some of the most sensitive contemporary issues that her liberal and fundamentalist characters might encounter. She addressed the Holocaust in her story "The Displaced Person", racial integration in "Everything That Rises Must Converge" and intersexuality in "A Temple of the Holy Ghost." Her fiction often included references to the problem of race in the South; occasionally, racial issues come to the forefront, as in "The Artificial Nigger," "Everything that Rises Must Converge," and "Judgment Day," her last short story and a drastically rewritten version of her first published story, "The Geranium."
Despite her secluded life, her writing reveals an uncanny grasp of the nuances of human behavior. O'Connor gave many lectures on faith and literature, traveling quite far despite her frail health. Politically, she maintained a broadly liberal outlook in connection with her faith, voting for John F. Kennedy in 1960 and supporting the work of Martin Luther King Jr. and the civil rights movement.