Memory serves as the predominant theme in the novel. Elhanan believes that the memory of the rape disrupts his memory, preventing him from honoring his heroic father, also named Malkiel. Elhanan believes that his loss of memory hinders him from keeping alive his father and other Holocaust victims and thus from obeying God. The memory of the dead, especially those who perished during the Shoah, is sacred. When he sends Malkiel to Romania, he insists that the son keep the memory of the massacres at Feherfalu locked inside his mind forever. Speaking of the victims who had once been his neighbors and friends, Elhanan says to Malkiel, "Remember, my son. Without even knowing it, I must have walked across their graves."

Jewish mysticism is another important theme in The Forgotten. Hershel, the gravedigger, and Ephraim, the blind seer and eternal crier, play significant roles in that they serve as the bridge between the past and the present. Although they may seem unpleasant and moody, through their gifts they help Malkiel in his journey. Hershel becomes Death personified and Ephraim labels himself Memory personified. The Great Reunion becomes important because it manifests the religious history of Feherfalu. Despite the great atrocities committed during the Holocaust, Hershel retains his faith in God and in the great rabbis of the community, indicating that the Jewish faith will survive despite the Holocaust. Hershel and Ephraim live on to ensure that the Jewish faith in this shtetl in the Carpathian Mountains will survive.

The element of forgiveness plays a significant role in the text. Elhanan believes that God has not forgiven him for leaving the Nyilas's wife when he could have saved her from Itzik the Long. God punishes him, Elhanan believes, because he has not sought the forgiveness of the woman, Elena Calinescu. Because he cannot travel due to ill health, Elhanan sends his son to Feherfalu to find the woman and seek forgiveness for him. Elhanan can only feel at peace when he knows that she understands his remorse for failing to intervene on her behalf.

Sexuality plays a part in this novel in that Malkiel's lust for women manifests his immaturity. As long as he has lusty feelings for women, his attempts to aid his father become impotent. Only when he can ignore the sexual advances of women such as the beautiful translator Lidia can he become focused and aid his father. By drinking with the hideously ugly Hershel rather than the attractive Lidia, he finds the clues that he needs in order to find out the truth about Itzik the Long and his cruel rape of Elena Calinescu.