Decades of mismanagement and years of UN sanctions were capped by unchecked looting and destruction after the US-led invasion of March 2003. Occupation officials later promised to set the reeling sector back on its feet.
The US former senior adviser to the Iraqi Ministry of Higher Education, John Agresto, told an audience in Washington on 25 June that he was "encouraged" by the progress made in rebuilding the system.
But despite some positive developments, academics in Iraq complain the recovery has generally been too slow and in some respects non-existent.
"Nothing has changed here concerning equipment and facilities," says Dr Sadeer Saleh, head of the translation department at Mustansiriya University in Baghdad.
Walking carefully up a flight of crumbling stairs studded with dangerously protruding steel cables, Dr Saleh shows me the language laboratory.
Because of the summer recess, there are no students present. Thanks to looters who stormed the lab in April 2003, there are no computers, translation devices or televisions either.
Decline and fall
Academics admit Iraqi higher education, once among the best in the region, was in a troubled state before the war.
The formerly thriving sector suffered from political cronyism under Baath rule, the effects of the long Iran-Iraq war in the 1980s, and the pressure of UN sanctions imposed after the 1990-91 Gulf war.
Students have suffered years of
isolation and underfunding
The UN itself acknowledged that in the 1990s Iraqi intellectual life, especially in the fields of science and medicine, was being strangled by sanctions, through international isolation and the shortage of textbooks and journals.
In 1997, UNICEF calculated the UN Oil For Food programme was providing only 10% of Iraq's educational needs.
"Before the war, we had all sorts of problems," says Dr Saleh. "But when the US promised to improve things, we raised our expectations."
Those expectations have been largely dashed because under the former occupation chief Paul Bremer, insufficient money was spent to produce tangible results, official reports show.
Of the $18.4bn Washington provided last year for rebuilding Iraq, only $366m - about two per cent - has been used, a White House report admitted on 28 June.
"To be honest, we
didn't get any help
from the Americans"
Dr Taki Ali al-Musawi,
"To be honest, we didn't get any help from the Americans," says Dr Taki Ali al-Musawi, the vice-president of Mustansiriya University, Baghdad's second biggest with around 37,000 students.
"They did help schools but they didn't give anything to universities. No money, no books, no equipment, just promises."
Other universities tell a different story but no one gives Bremer high marks for effort. At Baghdad University's department of politics, Dr Abd al-Jabbar Ahmad Abd Allah says the main campus luckily escaped looting because it was near other sites that the US sent troops to protect.
"Some of our other colleges suffered and our institution received some money from the Americans to replace the losses," says Dr Abd Allah, describing the extent of restoration to date as "50-50".
The Iraqi interim government has thus inherited a challenging task. The looting and destruction was not limited to Baghdad; universities from Basra in the south to Mosul in the north were ransacked.
US officials visiting the library at Tikrit University's law college reported seeing fewer than 80 volumes left on shelves built to hold up to 5000. Some texts were merely photocopies of photocopies.
Two students pass a US soldier on
guard at Baghdad University
Students told Aljazeera.net that war-time looting and raids by US troops not only disrupted their studies, but affected them psychologically too by violating the apparent sanctity of their campus.
"I was attacked by about 10 looters in my dormitory one night," recalls Muhsin al-Jurani, a student at Mustansiriya's translation department. "After that, I got a gun to protect the place."
"Everything was stolen, equipment, books even the telephone wires, and up to 80% of our buildings were burned and damaged," says Dr al-Musawi. "The new government faces a big problem - it doesn't have a magic wand."
But he is hopeful. The new higher education minister, Tahir al-Baka, was until recently the president of Mustansiriya and understands universities' needs, his former deputy says.
Faced with the devastation of their universities, academics, students and concerned Iraqis worked to rebuild their institutions.
"People contributed money, or donated books and furniture - this table was a donation," says Dr al-Musawi, tapping his desk. It was local money and effort that repaired the university's wrecked buildings, he says.
Some help has come from outside too. The United Nations Educational, Scientific and Cultural Organisation (UNESCO) and the Qatar Foundation launched an initiative in October 2003 to help rebuild Iraq's universities. Qatar made a first donation of $15m.
In the case of Mustansiriya, South Korea helped set up an internet system. Seoul has pledged $5m in computer equipment, training, and satellite time for Iraq's universities.
Kuwait recently provided $3m worth of textbooks, while US computer giant IBM has set up a partnership with Baghdad's University of Technology.
And in a bizarre twist, a few looters took pity on the teachers and students they had robbed and returned some stolen items, Dr al-Musawi says.
He admits, however, that academics now enjoy freedoms unthinkable under Saddam Hussein.
Campuses have seen protests
over US policies and operations
"We can now hold elections for academic posts. We're free to plan and negotiate," he says. "You don't feel you have to belong to a certain party.
"Before, we had the wrong people in the wrong jobs. Sometimes students were accepted on courses for the wrong reasons. But now we can judge people only on their abilities, experience and qualifications."
Once subject to tight central government control, university heads have been given more autonomy to develop their own curricula, experiment with teaching techniques, and acquire aids and equipment from any source.
But some at Mustansiriya claim that freedom has come at a cost and express anger, not appreciation. US soldiers in March 2004 attacked students protesting at civilian deaths from US-led assaults on Najaf and Falluja, said Ghazi Shanduk, a history undergraduate.
Others said US troops seized several computers during one raid, saying they were being used by supporters of opposition Shia leader Muqtada al-Sadr - a charge the students denied.
Iraq once boasted one of the region's best education systems, which was free at all levels. Iraqi academia's present predicament is all the more dismaying considering the country's rich heritage of scholarship.
Enrolment has risen by 50% since
the US-led invasion
In the early medieval period, Iraq-based scholars created a golden age of arts and science while Europe groped in benighted ignorance.
Even in more troubled recent times, Iraq has enjoyed some successes.
Literacy soared under a compulsory reading programme in the 1970s, ironically earning Saddam Hussein an award from UNESCO. Adult literacy reached 95% before UN sanctions were imposed.
Today, about 350,000 students attend 22 universities plus 42 technical institutes. Enrolment for first year students at colleges and universities rose from 60,000 before the invasion to 90,000 in 2003-2004.
"It has been a real challenge," says al-Musawi, noting the risks his staff face amid a still perilous security situation. "But we must rebuild Iraq and our universities, even if it costs us our lives."