The theme prejudice is presented throughout the whole book.
Along with struggling with concepts of good and evil, Scout and Jem spend a great deal of time trying to understand what defines and creates social strata. Scout tends to believe that "folks are just folks", while Jem is convinced that social standing is related to how long people's relatives and ancestors have been able to write.
Scout elucidates the town's social strata quite clearly on her first day at school when Walter Cunningham does not have lunch or lunch money. Her classmates ask her to explain to the teacher why Walter won't take a loaned quarter to buy lunch, and she lectures the teacher on the Cunningham's financial situation and how they trade goods for services. Scout and the other children have a very clear understanding of the social inequalities in their town, but see these inequalities as natural and permanent. The Finch family falls rather high up in the social hierarchy, while the Ewell family falls at the bottom. However, this hierarchy only includes white people. Maycomb's black population fall beneath all white families in Maycomb, including the Ewells, whom Atticus labels as "trash".
Scout understands this social structure, but doesn't understand why it is so. She believes that everyone should be treated the same, no matter what family they are from. For instance, when she wants to spend more time with Walter Cunningham, Aunt Alexandra objects saying no Finch girl should ever consort with a Cunningham. Scout is frustrated by this, as she wants to be able to choose her own friends based on her definition of what makes a good person: morality.
Obviously, racism is a major theme of the novel. During the Depression era, blacks were still highly subjugated members of society. Blacks were not permitted to commingle with whites in public settings, as exemplified in the courthouse physical separation of races and in the clearly distinct black and white areas of town. Moreover, things like intermarriage were almost unheard of, and sorely looked down upon.
Throughout the novel, Scout explores the differences between black people and white people. She and Jem attend church with Calpurnia and Scout truly enjoys the experience. Afterwards, she asks Calpurnia if she might be able to visit her house sometime because she has never seen it. Calpurnia agrees, but the visit is never made, largely because Aunt Alexandra puts a stop to it. Jem, Scout and Dill also sit with the black citizens of the town in the balcony of the court house to observe the trial. In addition, Scout and Dill have a lengthy conversation with Mr. Raymond, a white man who married a black woman and has mixed children. Mr. Raymond reveals that he pretends to be an alcoholic by carrying around a paper bag with a bottle of Coca-Cola inside in order to let the town excuse his choice to marry a black woman.
Tom Robinson is convicted purely because he is a black man and his accuser is white. The evidence is so powerfully in his favor, that race is clearly the single defining factor in the jury's decision. Atticus fights against racism, and a few other townspeople are on his side, including Miss Maudie and Judge Taylor. Jem and Scout also believe in racial equality, but are obviously in the minority. When Atticus loses the trial, he tries to make his children understand that although he lost, he did help move along the cause of ending racism as evidenced by the jury's lengthy deliberation period. Usually, such a trial would be decided immediately.
http://www.gradesaver.com/to-kill-a-mockingbird/study-guide/themes
