In coalition-occupied Iraqi territory, a peace conference was held where a ceasefire agreement was negotiated and signed by both sides. At the conference, Iraq was authorized to fly armed helicopters on their side of the temporary border, ostensibly for government transit due to the damage done to civilian infrastructure. Soon after, these helicopters and much of Iraq's military were used to fight an uprising in the south. On March 1, 1991, one day after the Gulf War ceasefire, a revolt broke out in Basra against the Iraqi government. The uprising spread within days to all of the largest Shia cities in southern Iraq: Najaf, Amarah, Diwaniya, Hilla, Karbala, Kut, Nasiriyah and Samawah. The rebellions were encouraged by an airing of "The Voice of Free Iraq" on 2 February 1991, which was broadcast from a CIA-run radio station out of Saudi Arabia. The Arabic service of the Voice of America supported the uprising by stating that the rebellion was well supported, and that they would soon be liberated from Saddam.

In the North, Kurdish leaders took American statements that they would support an uprising to heart, and began fighting, hoping to trigger a coup d'état. However, when no US support came, Iraqi generals remained loyal to Saddam and brutally crushed the Kurdish uprising and the uprising in the south. Millions of Kurds fled across the mountains to Turkey and Kurdish areas of Iran. On April 5, the Iraqi government announced "the complete crushing of acts of sedition, sabotage and rioting in all towns of Iraq." An estimated 25,000 to 100,000 Iraqis were killed in the uprisings. These events later resulted in no-fly zones being established in northern and southern Iraq.

In Kuwait, the Emir was restored, and suspected Iraqi collaborators were repressed. Eventually, over 400,000 people were expelled from the country, including a large number of Palestinians, because of PLO support of Saddam. Yasser Arafat didn't apologize for his support of Iraq, but after his death Mahmoud Abbas formally apologized in 2004 on behalf of the PLO. This came after the Kuwaiti government formally forgave the group.

There was some criticism of the Bush administration, as they chose to allow Saddam to remain in power instead of pushing on to capture Baghdad and overthrowing his government. In their co-written 1998 book, A World Transformed, Bush and Brent Scowcroft argued that such a course would have fractured the alliance, and would have had many unnecessary political and human costs associated with it.