During the first 25 years of the occupation, residents of the West Bank and Gaza Strip were able to move reasonably freely between the two parts of the Occupied Territories through Israel. This was made possible by general permits issued by the military regarding entry and exit from the Territories. The outbreak of the first intifada in 1988 saw a change in Israel's policy. First, the general entry permits were cancelled and, as a result, Palestinians who wished to travel from one area to the other were required to apply to the military commander of each area for a personal entry permit. In February 1991, during the First Gulf War, Israel changed the order permitting exit from the Territories. The general permits were cancelled and the residents of the West Bank and Gaza Strip were required to apply for personal permits in order to leave the area where they lived. The cancellation of the general exit permits marked the beginning of Israel's closure policy. In 1993, the military commander issued another order canceling the personal exit permits. In practice, this order, which has been continuously renewed, established the "general closure" of the Territories in effect to this day.
The territories of the West Bank and Gaza Strip, despite being physically separate, constituted a single political unit prior to the peace process owing to the national identity shared by the residents of the two areas, their common history prior to 1948, and the integration processes the two areas have undergone since the beginning of the occupation in all aspects of life: family ties, education, culture and economy. Israel has administered the regime of the occupation in the two areas in a similar and coordinated way, yet only in the framework of the 1993 Declaration of Principles and later in the Interim Agreement signed by Israel and the Palestinian Authority in 1995 (the "Oslo Accord"), did Israel acknowledge that the two parts form one unit. Additionally, in the Interim Agreement, the Palestinian Authority was defined as the Palestinian leadership in the Gaza Strip and West Bank and the two parts were recognized as a single territorial unit in which the Palestinian people's right to self-determination would be realized.
The Supreme Court reinforced this principle in its judgment in HaMoked's petition in the Ajuri matter (HCJ 7015/02), when it ruled that forcibly removing residents of the West Bank to the Gaza Strip does not constitute deportation but rather assigned residence in the same occupied area, as defined in article 78 of the Fourth Geneva Convention. This being the case, residents of the West Bank and Gaza Strip are entitled to freedom of movement between these two parts and all it entails. This fundamental right, which is parallel to an individual's right to move freely inside his own country, is well established in international humanitarian and human rights law as well as Israeli constitutional law. The right to freedom of movement may be restricted for security reasons. However, imposing sweeping disproportionate and unreasonable restrictions, as Israel has been doing regarding movement between the West Bank and Gaza Strip since the beginning of the second intifada, is a clear violation of international and Israeli law. It is worth noting at this point that as far as travel of Palestinians between the Gaza Strip and West Bank is concerned, Israel controls only the perimeter of the two parts. That is, in the absence of an assigned residence order, Israel may only limit entry into its territory for the purpose of traveling between the two parts of the Occupied Territories, but it cannot limit travel between the two parts per se – this is HaMoked's position.
The obligation to allow passage between the Gaza Strip and West Bank stems also from the right recognized in public international law as the right of transit. A state must allow passage in its territory to foreign subjects wishing to travel to a different country when such passage is required but will cause no harm to the state through which they transit. This obligation exists even when there are alternative travel options. A divided territory, such as the Palestinian territory, is among the cases which contributed to the development of the principle of the right of transit.
As part of the peace process, the parties agreed to establish a safe passage running through Israel which Palestinians may use to freely move between the Gaza Strip and West Bank. One of the routes of the "Safe Passage" was first opened in October 1999. According to the agreement, those wishing to use the passage required Israeli permits and those who were considered "barred entry" were allowed to travel only in secured buses. The "Safe Passage" operated for about one year only. When the second intifada broke out Israel closed the passage and its operation has not been resumed since.
Since the outbreak of the second intifida at the end of 2000, Israel has tightened restrictions on movement between the Gaza Strip and West Bank still further. Israel often imposes complete closures during which no exit or entry into or out of the Gaza Strip and West Bank is allowed. From time to time, Israel decides to completely prevent movement of certain age groups between the two parts. Additionally, a person's registered address as it appears in the population registry plays a crucial role in restrictions on movement. The Oslo Accord transferred the authority to manage the Palestinian population registry to the Palestinian Authority. This includes the authority to update changes of address. In order to assure that Israel has an exact copy of the Palestinian population registry, it was determined that the Palestinian side must inform the Israelis of all changes it makes in the registry retroactively. However, the authentic registry is the one managed by the Palestinian Authority. It must be noted that the Oslo Accord contains no special reference to changes of address between the Gaza Strip and West Bank.
In 2000, Israel decided to halt updating changes of address between the Gaza Strip and West Bank in its copy of the population registry as part of its general goal to separate between the West Bank and Gaza Strip. The information contained in the registry at that time was frozen with no possibility to change, amend or challenge it. This resulted in a discrepancy between the original Palestinian registry and the copy held by Israel; and Palestinians living in the West Bank whose registered address is in the Gaza Strip or vice versa have been detained as "illegal aliens." In fact, Israel is restricting freedom of movement based on the address appearing in its copy of the population registry regardless of where a person actually lives. 
Over the years, HaMoked has filed many HCJ petitions demanding Israel lift individual restrictions on movement it had imposed on Palestinians wishing to travel between the two parts of the Occupied Territories. The petitions dealt with, inter-alia, passage for the purpose of undergoing medical exams, visiting deportees and family members and studying in university, as well as in cases where passage was required as a result of having changed domicile. Many of these petitions were accepted and the restrictions on movement lifted.
In March 2006, HaMoked filed a petition dealing with general issue of the sweeping restrictions Israel imposes on the movement of Palestinians between the West Bank and Gaza Strip. The petition was deleted after the Court refused to hear it on the grounds that it challenged a general policy.