Afghanistan was a military quagmire for the Soviet Union, and Moscow's withdrawal of forces in 1988 led to a period of instability that resulted in the rise of the Islamic fundamentalist Taliban regime and the eventual U.S.-led invasion of the country in 2001. Following the 1991 Soviet coup against Mikhail Gorbachev, an agreement was reached between Moscow, Washington, and the main mujahideen groups that called for the cessation of external military assistance and the concurrent creation of an interim government, along with plans for future elections. However, various factions immediately commenced a civil war, which lasted until 1996 when the predominately Pashtun Taliban took control of 90 percent of the country. The remaining 10 percent, mainly in the northeast of the country, was under the control of the anti-Taliban Northern Alliance, composed mainly of ethnic Tajiks and Uzbeks. In 1997, the Taliban renamed the country the Islamic Emirate of Afghanistan. Only Pakistan, Saudi Arabia, and the United Arab Emirates granted diplomatic recognition to the Taliban.

The Taliban was led by the reclusive Mullah Mohammed Omar (1959-). It initiated a strict theocratic regime based on Sharia (Islamic law). Women's rights were limited. For instance, they could not appear in public without a veil or burqa. In addition, there were harsh penalties, including execution, for crimes, and music and films were banned. The Taliban also welcomed the Al Qaeda terrorist group, led by Osama bin Laden, into Afghanistan. Al Qaeda established a network of training camps throughout the country. In 1998, the United States conducted strikes with cruise missiles on suspected Al Qaeda sites in retaliation for the embassy bombings on American sites in Kenya and Tanzania. The United States endeavored to pressure the Taliban to turn over bin Laden, but Washington also granted the regime more than $200 million per year in aid from 2000 to 2001 to help eradicate poppy production. Afghanistan was the world's largest producer of heroin until the Taliban launched a program to stop cultivation in 1999.

After the September 11 terrorist attacks, the George W. Bush administration demanded that bin Laden and his terrorist network be disbanded and handed over to the United States for prosecution. The Taliban refused, and America led a multinational military coalition in an invasion of Afghanistan, designated Operation Enduring Freedom. The allies also supplied weapons and equipment to the Northern Alliance and carried out air and missile strikes against the Taliban. The regime was overthrown, and the senior Taliban and Al Qaeda leaders were killed, captured, or fled the country (Mullah Omar and bin Laden reportedly escaped to Pakistan).

A transitional government was created under moderate Pashtun leader Hamid Karzai, who was subsequently appointed interim president in 2002 by a Loya Jirga (a traditional council of ethnic and religious leaders). A United Nations peacekeeping mission was deployed alongside U.S. and coalition forces. However, regional leaders retained significant political and economic power that limited the authority of Kabul. By 2003, Afghanistan was again the world's leading poppy producer. In 2004, Karzai was elected president in the country's first free and democratic balloting. In 2006, in response to increased terrorist attacks and Taliban insurgent attacks, the North Atlantic Treaty Organization took command of an expanded peacekeeping mission.