He is married to Mira Nair, the Indian film director and producer. They met in Kampala, Uganda, in 1989 when Nair was researching for her film, Mississippi Masala. She had read his book The Myth of Population Control while an undergraduate at university and From Citizen to Refugee just before their meeting. They married in 1991 and have a son, Zohran Mamdani, who is running for NY State Assembly in Queens, NY in 2020.