In April 10, the day after Saddam Hussein's regime collapsed and Baghdad was in the hands of US military forces, looters brandishing iron bars forced their way into the National Museum of Iraq. Half a mile down the road, US troops turned a blind eye, choosing instead to protect Iraq's oil ministry.

When the world's media entered the building and found the place cleaned out - empty exhibition boxes and storerooms wherever they looked - there was international outrage, and reports that almost all of the museum's 170,000 artefacts had been either stolen or damaged. The museum had housed some of humanity's earliest documents and treasures dating from 7000BC to AD1000, charting the achievements and histories of the Uruk, Sumerian, Babylonian, Assyrian, Persian and early Islamic civilisations.

"The crime of the century," cried Donny George, director of research at Iraq's State Board of Antiquities, while others spoke of "cultural genocide" and compared the Americans to the Mongol invaders of 13th-century Iraq.

But in the weeks and months that followed, a very different picture of what happened to Iraq's lost treasures began to emerge. In the dark, damp vaults of the bombed-out Iraqi central bank, for instance, Americans cracked open five waterlogged wooden crates, peered inside and breathed a collective sigh of relief. There, in dozens of smaller boxes, were the world-famous treasures of Nimrud, "Iraq's crown jewels" - 613 pieces of gold jewellery, precious stones and ornaments from the height of the Assyrian civilisation in 800BC. Incredibly, they had survived a US missile strike, a flood, and the attention of desperate looters.

At the museum, too, tens of thousands of artefacts, including Sumerian bronzes, Babylonian tablets and Assyrian statuettes, were found in five specially designed "strongrooms". The museum staff, it turned out, had safe-housed most of the collection in the weeks leading up to the invasion. Some 40,000 ancient manuscripts, books and scrolls were also spirited away to a nearby bomb shelter, while senior members of the museum staff stashed precious artefacts in their own homes for safekeeping.

Other pieces were returned by the looters themselves after an amnesty was offered. In June, an old car pulled up outside the museum and three men in their twenties stepped out with a broken object wrapped in a blanket. It was the Sacred Vase of Warka, a 5,200-year-old limestone bowl, one of the greatest treasures of Mesopotamian antiquity. They handed it to the astonished museum officials, who said, "Thank you," no questions asked, and the men drove away. (Selling this well-known object on the black market would have been problematic.) Just this month, Iraqi investigators found the 5,200-year-old Lady of Uruk, sometimes called the Mona Lisa of Warka, a marble mask from ancient Sumer and one of the earliest representations of the human face. She was buried in a looter's garden in a small town north of Baghdad.

Officials are still trying to find around 3,000 artefacts missing from the museum, of which 30 or so are considered highly significant items, probably stolen by professional thieves, according to Donny George. "I'm not so optimistic about them, because I believe they were taken by professionals. They are out of the country now," he said recently.

Many of the recovered items have been damaged, such as the Vase of Warka, which was returned in 14 pieces by its looters. And many artefacts may never be recovered at all, as they were probably stolen several years ago by senior figures in the Ba'ath regime: Saddam's eldest son, Uday, is known to have made millions from the international trade in antiquities. "The Iraq museum was the only museum in the world that had a complete chain of human history starting half a million years ago to the beginning of last century," says George. "These items were very important links in that chain. Now they are missing and that is a great loss - not only for the museum, but for the whole of humanity."