A shekara ta 1929, Khomeini ya auri Khadijeh Saqafi, 'yar shekara 16 da wani malamin addini a Tehran. A duk asusun aurensu ya kasance mai jituwa da farin ciki. Ta mutu a shekara ta 2009. Suna da 'ya'ya bakwai, kodayake biyar ne kawai suka tsira da jariri. 'Ya'yansa mata duk sun yi aure a cikin' yan kasuwa ko dangin malamai, kuma duka 'ya'yansa maza sun shiga cikin addini. Mostafa, babban dan, ya mutu a shekara ta 1977 yayin da yake gudun hijira a Najaf, Iraki tare da mahaifinsa kuma magoya bayan mahaifinsa sun yi jita-jita cewa SAVAK ne ya kashe shi. Ahmad Khomeini, wanda ya mutu a shekara ta 1995 yana da shekaru 50, an kuma yi jita-jita cewa ya zama wanda aka kashe, amma a hannun mulkin.
Khadijeh Saqafi