As a result of the war, a wave of Palestinians was displaced. An estimated 300,000 Palestinians left the West Bank and Gaza, most of whom settled in Jordan.

In his book Righteous Victims, Israeli "New Historian" Benny Morris writes:

In three villages southwest of Jerusalem and at Qalqilya, houses were destroyed "not in battle, but as punishment ... and in order to chase away the inhabitants ... ---contrary to government...policy," Dayan wrote in his memoirs. In Qalqilya, about a third of the homes were razed and about 12,000 inhabitants were evicted, though many then camped out in the environs. The evictees in both areas were allowed to stay and later were given cement and tools by the Israeli authorities to rebuild at least some of their dwellings. But many thousands of other Palestinians now took to the roads. Perhaps as many as seventy thousand, mostly from the Jericho area, fled during the fighting; tens of thousands more left over the following months. Altogether, about one-quarter of the population of the West Bank, about 200-250,000 people, went into exile. ... They simply walked to the Jordan River crossings and made their way on foot to the East Bank. It is unclear how many were intimidated or forced out by the Israeli troops and how many left voluntarily, in panic and fear. There is some evidence of IDF soldiers going around with loudspeakers ordering West Bankers to leave their homes and cross the Jordan. Some left because they had relatives or sources of livelihood on the East Bank and feared being permanently cut off. Thousands of Arabs were taken by bus from East Jerusalem to the Allenby bridge, though there is no evidence of coercion. The free Israeli-organized transportation, which began on June 11, 1967, went on for about a month. At the bridge they had to sign a document stating that they were leaving of their own free will. Perhaps as many as seventy thousand people emigrated from the Gaza Strip to Egypt and elsewhere in the Arab world. On July 2 the Israeli government announced that it would allow the return of those 1967 refugees who desired to do so, but no later than August 10, later extended to September 13. The Jordanian authorities probably pressured many of the refugees, who constituted an enormous burden, to sign up to return. In practice only 14,000 of the 120,000 who applied were actually allowed by Israel back into the West Bank by the beginning of September. After that, only a trickle of "special cases" were allowed back, perhaps 3,000 in all.(328-9)

In addition, between 80,000 and 110,000 Syrians fled the Golan Heights, of which about 20,000 were from the city of Quneitra. According to recent research by an Israeli daily Haaretz, much of the Syrian population was expelled from the territory by the Israeli army.

Jews in Arab countries

With the loss of Arab lands, the minority Jews living in the Arab world immediately faced persecution and expulsion, following the Israeli victory. According to historian Michael B. Oren,

mobs attacked Jewish neighborhoods in Egypt, Yemen, Lebanon, Tunisia, and Morocco, burning synagogues and assaulting residents. A pogrom in Tripoli, Libya, left 18 Jews dead and 25 injured; the survivors were herded into detention centers. Of Egypt's 4,000 Jews, 800 were arrested, including the chief rabbis of both Cairo and Alexandria, and their property sequestered by the government. The ancient communities of Damascus and Baghdad were placed under house arrest, their leaders imprisoned and fined. A total of 7,000 Jews were expelled, many with merely a satchel.