According to the Fédération Internationale des ligues des Droits de l'Homme (FIDH), from the beginning of the Second Intifada in 2000 through to April 2003, more than 28,000 Palestinians were incarcarated in prisons or prisoner camps. In April 2003 alone, there were more than 5,500 arrests.
In 1998, the number of Palestinians held in administrative detention began to gradually decline and averaged less than 20 from 1999 to October 2001. However, with the start of the Second Intifada, and particularly after Operation Defensive Shield, the trend was reversed, and the numbers began to steadily climb. In 2007, the number of Palestinians under administrative detention averaged about 830 per month, including women and minors under the age of 18. By March 2008, more than 8,400 Palestinians were held by Israeli civilian and military authorities, of which 5,148 were serving sentences, 2,167 were facing legal proceedings and 790 were under administrative detention, often without charge or knowledge of the suspicions against them. The main prisons in which Palestinian prisoners apprehended by Israel are held are in the Ofer Prison in the West Bank and the Megiddo and Ketziot prisons in Israel.
On 17 April 2008, the annual day of commemoration for Palestinian Prisoners, Adalah: The Legal Center for Arab Minority Rights in Israel, published a summary report of statistics noting that there were 11,000 Palestinian prisoners being held in prison and detention in Israel, including 98 women, 345 children, 50 members of the Palestinian Legislative Council, and 3 ministers of the Palestinian National Authority. Of these 11,000 Palestinian prisoners, 8,456 were from the West Bank, 762 from the Gaza Strip, 552 from Jerusalem, and 132 from within Israel itself.
The 1995 Interim Agreement on the West Bank and the Gaza Strip (also known as 'Oslo 2') calls for the release of Palestinian detainees, in stages, as part of a series of "confidence-building measures." Because the accords fail to call for the immediate release of all Palestinian prisoners, they have been criticized by for being out of step with the Geneva Conventions, which note that when an occupier withdraws from a given territory: "Protected persons who have been accused of offences or convicted by the courts in occupied territory, shall be handed over at the close of occupation, with the relevant records, to the authorities of the liberated territories." Upon the Israeli withdrawal from populated Palestinian centers in 1995, many of the Palestinian prisoners in military jails were transferred to jails inside Israel, in breach of articles 49 and 76 of the Geneva Conventions prohibiting deportations. From the signing of Oslo through to 2001, an additional 13,000 Palestinians were arrested, tried and/or convicted, and because there is no clause in Oslo prohibiting or pertaining to arrests made after the signing of the accords, those arrested after the signing of Oslo II in 1995 are excluded from the conditions outlined in the agreements to follow.
The 1998 Wye River Memorandum specified that Israel was to release 750 Palestinian prisoners, some 250 of which were released by the time of the Sharm el-Sheikh Memorandum in 1999. Wye 2 reduced the number of those who were to be released from 500 to 350, and these were freed by mid-October 1999. Israeli pledges to release an undetermined number of prisoners at the beginning of Ramadan were met, albeit belatedly, when 26 'security' prisoners, half of whom had a few months left to serve were released on 29 December. An additional seven prisoners from East Jerusalem were released the day following after protests from the Palestinian Authority, who had expected more. Further releases of Palestinian prisoners by Israel in 2000 included 15 in March 2000 and 3 in June 2000, as a "goodwill gesture".
In a meeting in Sharm el-Sheikh in February 2005, Israel pledged to release another 900 Palestinian prisoners of the 7,500 being held at the time. By the spring of 2005, 500 of these had been released, but after Qassam rocket attacks on Sderot on May 5, Ariel Sharon withheld the release of the remaining 400, citing the need for the Palestinian Authority to reign in militants.
On August 25 2008, Israel released 198 Palestinian prisoners in a "goodwill gesture" to encourage diplomatic relations and support Fatah leader Mahmoud Abbas. The Israeli government has also offered to release 450 Palestinian prisoners in exchange for Gilad Shalit, an Israeli soldier held by Palestinian militants in the Gaza Strip since June 2006.
In a July 2003 report by the FIDH that was presented to the UN Human Rights Committee, it was noted that "Israel does not recognize Palestinian prisoners as having the status of prisoners of war." In practice, it is the Israeli military that controls the conditions of detention and the administrative detention system allows for the imprisonment of an individual for up to 6 months, and this detention can be extended without the approval of a judge. The FIDH report also notes that, "In the case of administrative detention, the necessary conditions for the execution of a fair trial are far from being achieved given that the lawyers do not even have access to the evidence."
In 1997, the United Nations Committee Against Torture found that such methods constituted torture and were in breach of the Convention Against Torture and Other Cruel, Inhuman or Degrading Treatment or Punishment, a convention ratified by Israel in 1991. In September 1999, a ruling by Israel's High Court repudiated the Landau Commission's position, stating that the Israeli Security Agency (ISA) does not have legal authority to use physical means of interrogation that are not "reasonable and fair" and that cause the detainee to suffer. While the court noted that a reasonable interrogation is likely to cause discomfort and put pressure on the detainee, this is lawful only if "it is a 'side effect' inherent to the interrogation," and not aimed at tiring out or "breaking" the detainee as an end in itself.
Uri Davis writes that the Supreme Court ruling of 1999 came after 50 years of silence "in the face of systematic torture practiced in Israeli jails and detention centers against Palestinian prisoners and detainees, as well as other prisoners." However, Davis also notes that after the Supreme Court ruling, the Public Committee Against Torture in Israel reports that "torture has, in most cases, ceased."
In 2000, an official Israeli report has acknowledged that the Israeli security service tortured detainees during the First Intifada. The report said that the leadership of Shin Bet knew about the torture but did nothing to stop it. Human rights organisations say some detainees died or were left paralysed.
In Confronting the Occupation, Maya Rosenfeld, notes that in the 1980s, "Under the conditions that prevailed in the West Bank, the option of armed resistance was completely blocked, while organized political activity was completely obstructed by clashes with the military rule and took place under the permanent shadow of threat of arrests. The prisons, where so many were to undergo their punishment, were a 'sanctuary', if only because it was no longer possible to threaten their inmates with incarceration." Rosenfeld's research among Palestinian refugees in the Dheisheh camp in Bethlehem found that the politicization process of young men from the camp underwent a qualitative transformation during their period of imprisonment, which she attributes largely to the internal organization practices of Palestinian prisoners and the central role of studies and education. An Israeli investigation among Palestinian prisoners in the early stages of the First Intifada found that their political mobilization was not so much ideologically-based, as it was a function of repeated humiliations at the hands of Israeli forces.
On 1 May 2001, almost 1,000 of the 1,650 Palestinian prisoners being held in Israeli prisons at the time participated in a month-long hunger strike, in protest against "arbitrary treatment by prison officials, substandard prison conditions, prohibitions on family visits, use of solitary confinement, poor medical care, and Israel's refusal to release all the categories of prisoners specified in its agreements with the Palestine Liberation Organization (PLO)." Mass demonstrations in solidarity with the prisoners erupted throughout the areas of Palestinian self-rule in the days following, culminating in a mass protest on May 15 (the anniversary of the Nakba) and ending on May 18 with 7 Palestinians fatalities, 1,000 injuries and 60 Israeli wounded. The hunger strike was ended on May 31 after Israeli prison authorities promised to review the complaints and ease restrictions on visitations. A report by the Israeli government released in June 2001 on conditions in the Shatta prison noted that the living conditions were "particularly harsh" in the wing where prisoners from the Occupied Palestinian Territories were held, and concluded that the exposed tents and filthy bathrooms in which prisoners were housed and bathed were unfit for human use.