Background Access to health care is a fundamental human right and inadequate access can compromise health. Israel's military occupation of the West Bank and Gaza Strip and annexation of East Jerusalem, occupied Palestinian territory (oPt), in contravention of international law restrict the movement of Palestinians within and between these regions. Patients' access to specialised health care is hindered by difficulties in obtaining the permits required by the Israeli authorities and by restrictions on the modes and routes of travel, with increased cost, time, and difficulty caused by the blockade of the Gaza Strip, presence of Israeli settlements in the oPt, and separation wall around Jerusalem. We assessed the extent and effect of these barriers for Palestinian patients needing health care and for Palestinian service providers who encounter difficulties in travelling to work. Methods We used quantitative and qualitative approaches to describe and analyse the experiences of Palestinians in the West Bank and Gaza Strip who applied for permits from the Israeli authorities during 2011, either to access health care or for travel to work in Palestinian hospitals in East Jerusalem. Data for patient referrals were obtained from the Palestinian Ministry of Health; data for permit applications and responses were obtained from the Palestinian General Authority of Civil Affairs, West Bank and Gaza Strip, and hospitals in East Jerusalem. Permit data for the Gaza Strip were analysed by application response (classified as approved, denied, or delayed [appointment date]), age, sex, and residence; disaggregated data were not available for the West Bank. Data for ambulance access were obtained from the Palestinian Red Crescent Society, West Bank, and the Palestinian General Authority of Civil Affairs, Gaza Strip. Data for permit applications submitted between Jan 1 to March 31, 2012, at three district liaison offices, West Bank, with high denial rates were analysed to ascertain reasons for denial. We interviewed families of patients who died after applying for a permit but before they had access to health care. Data were limited by the absence of detailed information about patients on non-ministry referrals and permit applications, and the under-reporting of deaths and interviews of patients called for by the Israeli security authorities. Data were analysed with Microsoft Excel (versions 2007 and 2010). Verbal approval for use of data was obtained from the Palestinian Ministry of Health and General Authority of Civil Affairs. Patients and families gave verbal consent for interviews. We did not use patients' personal information. Findings In 2011, 33 285 patients (23 877 from West Bank and 9408 from Gaza Strip) referred by the Ministry of Health required Israeli permits for access to hospitals. Of these referrals, 24 168 (73%) were within the oPt, and 4764 (14%) to Israel and 4350 (13%) to Jordan. 175 228 patients and their companions in the West Bank applied for permits for health-care access in 2011; of these, 32 678 (19%; range 8–30% in 16 district offices) had their access permits denied or delayed. Data for the first quarter of 2012 from three district offices showed the most frequent reason given for denying patients was security (680 [42%] of 1622 denials). No criteria could be identified for denials on the basis of security. For the 1053 staff who needed permits to travel to work in hospitals in East Jerusalem, 986 staff received permits for 6 months, 46 for 3 months, and 21 were denied permits. All permits were restricted by mode and route of entrance to East Jerusalem. Only on 49 (5%) of 1074 occasions were ambulances permitted to enter East Jerusalem. In 2011, 1082 (10%) of 10 560 applicants in the Gaza Strip had their access permits denied or delayed, with no reason given, and 197 (2%) were called for security interview. Patients aged 18–40 years had the highest rate of denied or delayed permits. Tracer interviews with Gazan families of patients who had their permits denied or delayed showed that six patients died while waiting for the permits. Interpretation Our data provide quantification of the extent of restricted access to health care for Palestinians in the West Bank and Gaza Strip and show that procedures for obtaining permits required by the Israeli authorities cause substantial difficulties in the access to hospital care for patients. Further study is needed to ascertain how and to what extent these difficulties in access have an effect on the health status and wellbeing of the patients. Funding Swiss Development Cooperation.