The students' demand -- that the Afghan government deny permanent military bases to the United States -- brings the Koran issue into the country's political arena.
The students issued a declaration demanding that U.S. President George W. Bush apologize for the alleged desecration, and for the perpetrators to be tried in an Islamic court.
An Afghan student demonstrator, reading one of the declaration's key points, said: "Afghanistan is a free country, and the creation of permanent U.S. military bases [threatens] the independence and freedom of the people."
The student demands run counter to Afghan President Hamid Karzai's plans to form a "strategic partnership" with the United States.
Karzai claims that on 8 May he received the backing of more than 1,000 tribal elders and officials to proceed with such a partnership, which would likely include permanent American military bases in Afghanistan. Karzai and Bush are due to meet in Washington on 23 May.
Anger at the desecration allegations has been spreading in Afghanistan since a brief item first appeared in the U.S. "Newsweek" magazine. The report said the Koran had been placed on or in toilets at the detention facility in Cuba in an effort to coerce terrorist suspects into releasing information or giving confessions.
If the report is confirmed, U.S. officials have said the perpetrators will be punished.
Some Peaceful Protests
Mostly peaceful protests have occurred in as many as 10 Afghan provinces. The episodes of violence have been centered in the eastern province of Nangahar, and its capital, Jalalabad.
Malik Mohammad Omar, the head of Khogyani District in eastern Nangarhar Province, said two people were killed today in the district of Khogyani, near Jalalabad, in an exchange of gunfire between Afghan security forces and demonstrators.
Provincial Governor Haji Din Mohammad told RFE/RL he views the protesters as "people who do not want peace and stability" in Afghanistan.
"They even tried to cause some disorder before in these regions, but they could not succeed, and this time they abused the name of democracy and of demonstration and caused this problem," he said. "I can say that these are people who do want peace and stability in Afghanistan and since Nangarhar is one of Afghanistan's important provinces, they wanted to cause some unrest here."
Interior Ministry spokesman Luftullah Mashal said another person was killed in nearby Wardak Province during similar protests.
Today's violence comes one day after similar protests in Jalalabad also turned violent. Four people were killed and more than 70 others were injured in those clashes.
Demonstrators threw stones at homes, cars, and offices. They burned down the two-story government building. Then they set fire to offices of the United Nations and other international organizations. Afghan police and troops began shooting, killing up to four demonstrators and injuring some 70 others.
The UN says nonessential aid staff are being relocated from Jalalabad following the riots. United Nations spokeswoman Ariane Quentier criticized the Jalalabad events, saying the UN Afghan assistance mission "strongly condemns the episode of violence in Jalalabad yesterday, in which a number of civilians have been killed or injured, and deplores the brutal attacks perpetrated against the premises of UNAMA, other UN agencies, as well as governmental, nongovernmental, and private organizations."
Why did the protests in Jalalabad turn violent?
Afghan writer Ismail Yoon told RFE/RL's Afghan Service from Nangarhar that it's possible the violence is being instigated by disaffected political elements who now find themselves on the outside of the country's political process.
In other words, the allegations about the Koran -- though serious in themselves -- were an excuse to cause trouble for Karzai's government.
"Jalalabad has a big population, and this issue is a very sensitive religious issue," Yoon said. "Naturally, people get very excited and emotional when it comes to religious issues. It is possible that some people who had a hand in these demonstrations and organized them were aiming to create violence."
Wahid Mojhdeh is a political analyst in Kabul. He says tensions already existed in eastern Afghanistan between the local population and U.S.-led coalition forces. He says the allegations over the Koran simply inflamed those forces.
"A few weeks ago in several districts in the east of Afghanistan, coalition forces had entered people's houses without permission," Mojhdeh said. After the Koran allegations came to light, he added, the tension that already existed "was transformed into action and led to the violent demonstration."
Some observers also noted the inexperience of police and security forces in eastern Afghanistan. Sadiq Patman, the editor in chief of "Bayan" magazine and a Kabul-based political analyst, told RFE/RL's Afghan Service that both the police and the protesters are to blame.
"Both sides are responsible because demonstrations have some rules according to Afghan law. Demonstrations should be peaceful and without people carrying guns. According to my information, the demonstrators were even seen with guns," Patman said. "On the other hand, the police are responsible because it has been three years since the [government] was created in Afghanistan and all the world is helping it, but we haven't equipped our police with the tools that will enable them to end demonstrations peacefully -- for example, with the use of water cannons or the use of tear gas, which is a tool that can temporarily stop a demonstration."
Karzai said yesterday that the Jalalabad shootings showed the unpreparedness of Afghan security forces to handle civilian demonstrations, which he said are part of democratic life.
In a statement, the U.S. Embassy in Kabul expressed full confidence in the abilities of the Afghan security forces.
(Story by Golnaz Esfandiari and Breffni O'Rourke; RFE/RL's Afghan Service contributed to this report.)
Protests Turn Violent