In 1999, Barghouti traveled to the West Bank where he joined the Hamas paramilitary group. He is considered by Ynet as Hamas' "engineer", and designed and built weapons for numerous attacks against Israeli civilians. +more Among the attacks he was involved in was the Sbarro restaurant suicide bombing, the double suicide bombing in the Ben Yehuda pedestrian mall, the Café Moment bombing, the 2002 Rishon LeZion bombing, the Hebrew University bombing, the Allenby Street bus bombing, the Pi Glilot bombing attempt, and an attack on railway tracks in Lod in which he personally laid the explosive charge. A total of 66 Israelis were killed and 500 injured in attacks that Barghouti was involved in.
In late 2001, Barghouti was arrested by the Preventive Security Forces of the Palestinian Authority on late Palestinian President Yasser Arafat's orders over involvement in the Sbarro restaurant bombing. Following a deterioration in relations between the PA and Israel in January 2002, Fatah leader Marwan Barghouti lobbied Jibril Rajoub, chief of the PA security forces, to release Abdullah Barghouti. +more He returned to Hamas activities.
Barghouti was arrested by the Israeli Shin Bet security service in March 2003. An Israeli military court sentenced him to 67 life terms plus 5,200 years in prison. +more The sentence was the longest given out in Israel's history. Barghouti is incarcerated at Gilboa Prison near Beit She'an. He is held in solitary confinement and is not allowed family visits.
The Israeli government refused to release Barghouti as part of the 2011 Gilad Shalit prisoner exchange. The Palestinian Authority has paid Barghouti a pension throughout his imprisonment.