Gerrit Augustinus Siwabessy was born to clove farmers Enoch Siwabessy and Naatje Manuhutu in Saparua, a small island in central Maluku within the vicinity of Ambon.
During Siwabessy's first years as an undergraduate, he attended a conference of the local Studenten Vereniging Christen (Christian Student Association) which took place in Kaliurang, a small town within the vicinity of Yogyakarta.