Nearly every account of the Hypogeum says that the remains of about seven thousand people were found in it. The figure should be treated as an early estimate produced while the deposit was being removed, not as a count.
The complex was found in 1902 by workmen cutting a cistern for new housing at Paola, and they broke into it from above. The first clearance was directed by Manuel Magri, a Jesuit, who worked on it until he was posted abroad and died in 1907. His records were lost. That is the whole of the problem: the earliest and by far the most destructive phase of the excavation of one of the most important prehistoric sites in Europe has no surviving documentation at all. Themistocles Zammit took the work over, continued it to 1911, and published properly, but by then a great deal had already been shifted.
So the number rests on an estimate of bone volume made under conditions nobody can now check, and the burials themselves were commingled, disarticulated and stacked. The order of magnitude is probably right. The precision is not real.
The site itself is extraordinary and the description is not in doubt. Three levels were cut down into globigerina limestone over roughly fifteen hundred years from about 4000 BC, and the chambers imitate in carved rock the architecture that Malta's megalith builders were raising above ground: corbelled ceilings, trilithon doorways, lintels. It is a building made by removal rather than by stacking, which is what makes it unique. Red ochre spirals survive on some ceilings. The Sleeping Lady, a small clay figure of a woman lying on her side, came from here.
One modern claim needs separating out. The chamber called the Oracle Room is widely said to resonate at a specific frequency, often given as 110 Hz, with measurable effects on brain activity. Serious acoustic research on the site does exist and concerns the tuning of the chambers' geometry and how sound behaves in them. It does not establish a neurological effect, and researchers working on archaeoacoustics have written that the earlier studies these claims are built on lacked methodological rigour. The chambers do sound remarkable. That is as far as the evidence goes.
Access is now capped at eighty visitors a day in small timed groups, with temperature and humidity controlled, because human breath was damaging the ochre.