The story begins in 1941, when Elie was twelve years old and living in Sighet with his family. In spite of his youth, the Jewish Elie was eager to study the Talmud and Cabbala. His father, however, thinks Elie is too young for such advanced subjects and refuses to find him a teacher. As a result, Elie turns to Moshe the Beadle for guidance.
One day Moshe is arrested by the Nazis. When he returns, he tells the villagers about how he has miraculously escaped from his torturers. He also tells them shocking stories about the atrocities committed against the Jews by Hitler's regime. When Elie and the other villagers do not believe his stories, thinking he has gone mad, Moshe weeps and tells his story again.
As time passes, the Nazis treat the Jews worse and worse. First they shift the Jewish people to live in ghettos; then they arrest them and transport them to Birkenau, the reception center that leads to Auschwitz. Elie, his parents, and his sisters are arrested by the Nazis and sent by cattle car to Birkenau. During the journey, Elie, his family, and the other Jews suffer from the inhuman conditions they must endure; they are also driven to distraction by the hysterical screams of Madame Schachter, who has hallucinations of fire and furnace.
When Elie and his family arrive at the concentration camp, they see flames rising out of an oven, which is actually a crematorium for the prisoners. They are repulsed by the stench of burning flesh. Then Elie and his father are separated from his mother and sisters. In the men's camp, Elie fights to protect his father and is repeatedly tortured himself. Gradually he begins to lose faith in God because of the atrocities he must witness and endure. On the eve of Rosh Hashanah, a Jewish Holy Day, Elie refuses to pray.
In the camp, a regular process of selection takes place to separate the physically fit prisoners from the unfit or sick ones. The abler men are given a chance to work and live, while the weaker ones are sent to the furnaces to be killed. Both Elie and his father survive the selection process; but they know there is no guarantee that they will survive the work and brutality. They often watch other prisoners as they are hanged for some little offense. The Nazis even hang an innocent thirteen-year-old boy with an angelic face.
In January 1945, Russian liberation forces draw near Buna, the camp where Elie and his father are staying. As a result, the Nazis evacuate the camp and force the prisoners to run through the snow toward Gleiwitz; they do not provide them any food or water during the trip. Elie and his father are amongst the prisoners forced to make the journey; it is a particularly difficult trip for Elie, for he has recently had an operation on his right foot, due to an infection. Elie struggles to keep up the pace, for the prisoners who fall behind are shot by the Nazis; many others fall down and are trampled to death by other prisoners.
Finally, the prisoners are loaded into roofless cattle-cars and taken to Buchenwald in central Germany. Many people die during the journey because of exposure and starvation, but Elie and his father manage to survive. At Buchenwald, however, Elie's father grows very ill, suffering from dysentery and malnutrition. He is also cruelly beaten on his skull. Elie tries his best to nurse his sick father back to health, getting very little sleep himself.
One night Elie unwillingly falls asleep due to his total exhaustion. When he wakes up, he finds that his father is not in his bed. He suspects that he has been taken to the crematorium, while he was still breathing, for the Nazis would judge the sick, old man as worthless. Elie is left with a life long repentance that he did not look after his sick father until the last moment.
At the end of the book, the Allied forces arrive at the concentration camp and liberate the prisoners. Even though he is freed, Elie is physically and emotionally devastated from his year of imprisonment. Three days after his release, he becomes seriously ill and must be hospitalized. When he has recovered enough to get out of bed, Elie looks in the mirror and thinks that he looks like a corpse. He knows he will always be haunted by the horror he has endured; the memory will forever be like a dark and scary night to him.