The trio, all aged between 15 and 16, are accused of religiously motivated destruction of property, following the appearance of the graffiti last month.
Slogans left on walls of the Dormition Abbey and the Via Dolorosa street included "Christians to Hell", "Death to the heathen Christians, the enemies of Israel" and "May his name be obliterated" (thought to be referring to Jesus).
The youngsters are too young to be named.
The Dormition Abbey
- Also known as the Church of the Dormition.
- Current church and monastary were consecrated in 1906.
- Located on Mount Zion in Jerusalem.
- The place where the Virgin Mary died, according to Christian tradition.
Speaking after the graffiti appeared on January, 17, Carole Nuriel and Rabbi David Fox Sandmel from Anti-Defamation League said on the abbey's website: "This Church has been the target of repeated attacks.
"Sadly it is, but one of an increasingly long list of religious sites, including churches, mosques and synagogues that have been vandalized by Jewish extremists who reject the value of religious freedom enshrined in Israel's Declaration of Independence."
"While we acknowledge Israel's efforts to combat this extremism and call to bring the perpetrators to justice, we share the feeling expressed by many in the Christian community that enough is enough."