al-Khoei was married and had seven sons:
Jamal al-Din.
He was al-Khoei's eldest son, and spent his life in the service of his fathers marja'iya.
He passed away in Tehran after being diagnosed with cancer, in 1984.
He was buried in the Fatimah Masumah shrine in Qom.
His notable works are: Sharh Kifayat al-Usul, Bahth Fi al-Falsafa Wa Ilm al-Kalam, Sharh Diwan al-Mutanabi.

Ali al-Khoei.
He was killed young in a car accident between Baghdad and Najaf.

Abbas
Abd al-Sahib.
Current secretary general of the Imam al-Khoei Foundation in London.

Muhammad-Taqi.
He was the secretary general of the Foundation in 1989.
He was placed under house arrest with his father after the 1991 Shaban uprising.
Muhammad-Taqi was allegedly assassinated by Saddam Hussein, who set up a car accident, on the night of 21 July 1994.
Besides reports of his father's lectures, he has authored Kitab al-Iltizamat al-Taba'iya Fi al-Uqud.

Abd al-Majid.
He emigrated from Iraq soon after the Shaban uprising, and left for London.
He became the secretary general of the Foundation after his brother, Muhammad-Taqi's death.
Soon after the fall of Baghdad to US forces in 2003, he returned to Iraq with plans to revive Najaf to the glory and splendor it enjoyed under the patronage of his father.
However, he was assassinated on April 10, 2003, near the Imam Ali Mosque in Najaf.

Ibrahim.
He was abducted from his house by the Baathist regime after the Shaban uprising, in 1991.
al-Khoei was married and had seven sons:
Jamal al-Din. He was al-Khoei's eldest son, and spent his life in the service of his fathers marja'iya. He passed away in Tehran after being diagnosed with cancer, in 1984. He was buried in the Fatimah Masumah shrine in Qom. His notable works are: Sharh Kifayat al-Usul, Bahth Fi al-Falsafa Wa Ilm al-Kalam, Sharh Diwan al-Mutanabi.
Ali al-Khoei. He was killed young in a car accident between Baghdad and Najaf.
Abbas
Abd al-Sahib. Current secretary general of the Imam al-Khoei Foundation in London.
Muhammad-Taqi. He was the secretary general of the Foundation in 1989. He was placed under house arrest with his father after the 1991 Shaban uprising. Muhammad-Taqi was allegedly assassinated by Saddam Hussein, who set up a car accident, on the night of 21 July 1994. Besides reports of his father's lectures, he has authored Kitab al-Iltizamat al-Taba'iya Fi al-Uqud.
Abd al-Majid. He emigrated from Iraq soon after the Shaban uprising, and left for London. He became the secretary general of the Foundation after his brother, Muhammad-Taqi's death. Soon after the fall of Baghdad to US forces in 2003, he returned to Iraq with plans to revive Najaf to the glory and splendor it enjoyed under the patronage of his father. However, he was assassinated on April 10, 2003, near the Imam Ali Mosque in Najaf.
Ibrahim. He was abducted from his house by the Baathist regime after the Shaban uprising, in 1991.
Abu al-Qasim al-Khoei