Shi dai wannan yaro ya gaji iyaye da kakanninsa ne wadanda daya bayan dayansu suka dauki nauyin aikin shiryar da mutane da kuma neman ilmi. Mahaifi marigayi Imam Khumaini (r.a) shi ne Marigayi Ayatullah Sayyid Mustafa Musawi, daya daga cikin malaman da suka yi zamani da Ayatullah al-Uzma Mirza Shirazi (r.a). (A bisa al'ada) mahaifin Imam Khumaini ya tafi birnin Najaf na kasar Iraki don karatun addini inda bayan ya kai matsayin ijtihadi (matsayin iya ciro hukumce-hukumcen shari'a daga mabubbuga) sai ya dawo gida wato garin Khumain ya ci gaba da shiryar da mutane a can. A lokacin Imam yana shekara biyar mahaifinsa ya yi shahada sakamakon harin da aka kai masa a hanyarsa ta zuwa garin Arak saboda irin nuna rashin amicewar da yake yi da zaluncin mahukunta na wancan lokacin. Bayan wannan kisan gilla, danginsa da mutanen garin Khumain sun fito don nuna rashin amincewarsu, bayan haka kuma suka wuce zuwa birnin Tehran don isar da kukansu da bukatan da a zartar da hukumci (kisasi) a kan wadanda suka aikata danyen aikin. Wannan kisan gilla da aka yi wa mahaifinsa ya sanya Imam (r.a) tun yana karami ya fahimci dacin maraici da kuma ma'anar shahada. Don haka mahaifiyarsa (Banu Hajar) ita ce ta ci gaba da kula da kuma tarbiyantar da shi, kasantuwar ita ma ta fito ne daga madaukakin gida don kuwa ita jika ce wa Ayatullah Khunsari (marubucin littafin Zubdatul Tasanif) da kuma goggonsa (Sahiba Khanum). To sai dai lokacin da Imam ya kai shekaru 15 a duniya ya rasa irin wannan kulawa lokacin da wadannan masu kulawa da shi suka rasu.