At 16, Barghouti was arrested and deported by Israel. He returned to the West Bank and became president of the student body at Birzeit University. Deported again for advocating the cause of the Palestinians, he returned in 1993 with the Oslo Accords and was elected to the Palestinian Legislative Council, in which he advocated peace with Israel, sometimes coming in conflict with Yasser Arafat. The formal position occupied by Barghouti was the General Secretary of Fatah in the West Bank.
By the summer of 2000, Barghouti had fallen into Yasser Arafat's disfavor, and was to be fired shortly. As the Second Intifada began, Barghouti was arrested by Israel (April 15, 2002) and indicted in civilian court (August 14) on charges of responsibility for the terrorist activities carried out by forces under his supervision. The case continues at Aug 2003. The charges include: