In a cell inside São Paulo’s House of Detention, better known as Carandiru, two inmates (Lula and Dagger) have a score to settle. The atmosphere is tense. Another inmate, Black Nigger, a kind of "judge" for settling disputes among prisoners, solves the case in time to welcome the Doctor, who has recently arrived, eager to begin voluntary medical aid in the penitentiary.

The Doctor is faced with extremely serious problems inside this, Latin America’s largest jail: overcrowded cells, decaying facilities, diseases such as TB, leptospirosis, cachexia, and the beginnings of an AIDS epidemic. The inmates have access to neither medical care nor legal assistance. Carandiru, with upwards of seven thousand prisoners, is a huge challenge for the newcomer. But after working there for a few months he perceives something that will transform him: the inmates, even in this appalling situation, are not demonic figures. In his daily contacts with the prisoners who see him in his makeshift office, the Doctor witness’s solidarity, organization, and above all, a great will to live.

Although he is a famous oncologist, accustomed to working with the most advanced technology, the Doctor has to practice rudimentary medicine, with a stethoscope, his feeling, and a good deal of talking and listening. His work begins to bear fruit, and the Doctor earns the respect of the inmates. And with respect come secrets. His consultations begin to deal with issues beyond disease; the inmates start to tell him their life stories. His meetings with patients in the ward become "windows" into the world of crime.

The narratives are reconstructed through flashbacks. Zico and Deusdete, inseparable friends since childhood and adolescence, come to a tragic end in the jail. Highness, the drug-dealer, swaggers around the jail, and enjoys the favors of his two women, Dalva and Rosirene. Old Chico, who has acquired wisdom in solitary confinement, loves making elaborate balloons and is about to be released, when he will see his 18 children again. The "judge," Black Nigger, the leader of all the inmates, has so many problems to deal with that the Doctor produces an unexpected diagnosis for him: stress. The hit man Dagger, convicted 39 times, undergoes a noisy conversion to religion and becomes an evangelical priest. The surfer Ezequiel plays out his own rise and fall in the jail. Friends and bank robbers Antonio Carlos and Claudiomiro fall out over the cunning and perverse Dina. The existentialist "philosopher" No Way has a fairy tale love affair with the divine Lady Di. The Chief Warden, Sr. Pires, has his work cut out to manage the jail.

The film’s narrative is like a jigsaw. One story fits into another to paint a realistic portrait of the tragedy of Brazil. Along with the Doctor, the viewer follows the daily routine of the inmates leading up to the terrible 2nd of October, 1992 – the day that shook the Casa de Detenção (and all Brazil): the Carandiru Massacre.