There are two significant main characters in The Boys from Brazil, a novel that posits the unsettling possibility that Nazis could use emerging technology (cloning) to create a new living version of Hitler, the German leader who ordered and orchestrated the Holocaust during World War II. One character is Josef Mengele, Hitler's right hand man, known as the "Angel of Death" for his pragmatic and cold-blooded approach to the capture, torture, and murder of millions of Jews and others at several camps in Germany.

In real life, Mengele, a fugitive from justice after the war, died in the late 1970s in South America. The novel imagines what might have occurred if Mengele had survived—and with him, the ideology of hate and dysfunctional racial purity that allowed the Third Reich to come to power. Mengele's plot is carried out beginning in Brazil, hence the title. He oversees plans to clone Hitler's genetic material and create a number of boys who will be raised in households similar to Hitler's own upbringing, in secret locations throughout the world and without the parents being made aware of who their adopted children really are. The boys are to be closely followed as they mature, and one will be selected to be groomed as the new leader. Mengele is portrayed as charismatic and compelling; played by Gregory Peck in the 1978 film version, he is soft spoken but also prone to fits of anger. He has his hair dyed black, a sign of vanity in an elderly man.

An investigative journalist named Barry Kohler is also a crucial character, though he is not part of the story for very long. He is researching the Third Reich and surviving adherents of Nazi ideology, as well as escaped war criminals. In doing his work, he stumbles upon the plot to clone Hitler. He contacts Yakov (Ezra) Liebermann, a well known Holocaust scholar and Nazi hunter, to help him expose this plot. Before he can provide evidence to Liebermann, he is mysteriously killed.

Liebermann is the other main character in this story. He understands Kohler's death was no accident and that he would be in grave danger also if he pursued this mystery. But as an experienced mercenary and a man motivated to root out the evil of the Nazi legacy, Liebermann pushes forward, despite his advanced age. Played by Lawrence Olivier (considered one of the finest English actors of all time), Liebermann has a quiet intensity and is very observant of everything around him. He eventually manages to find several of the "boys" born/created in Brazil at their new homes, where they are being raised by unsuspecting families and under the close watch of Nazi operatives.

The "boys," mostly located in the United States but also in Europe, are also an important set of characters. In the film version, they are all played by the same actor, because they are physically identical. They seem to share personality traits as well. Liebermann is struck each time he meets one of them by not only their physical similarities but the types of people they seem to be. He realizes that one of them could indeed be made into a modern day Hitler. The last "boy" is found in California and is obsessed with making movies. He owns a number of German Shepherds that have been trained as attack dogs, and the commands he uses are film making terms like "action" and "cut." This detail is particularly chilling if one recalls that Hitler himself was an ardent animal lover, despite his other proclivities.

Liebermann finds it difficult to carry out plans to execute the boys, despite knowing that it's the wisest decision. This personal moral dilemma informs the suspense of the plot in both the novel and the film.