Behind the circular chamber and across the passage just referred to lies a small room which, rightly or wrongly, has been called the ’Holy of Holies,’ the idea being that it formed a kind of inner sanctuary to the chamber.  It contains a rough shelf cut in the wall, and in the centre of this a shallow circular pit.  It has been suggested that this pit was made to hold the base of the cult-object, whether it was a baetyl or an idol.  This, however, is a mere conjecture.  In the passage just outside the door of this room are two small circular pits about 6 inches in diameter and the same distance apart.  They connect with one another below, and are closed with tightly fitting limestone plugs.  In one of them was found a cow’s horn.  Their purpose is unknown, but similar pairs of pits occur elsewhere at Halsaflieni.

In two of the largest chambers in the hypogeum the roof and walls are still decorated with designs in red paint.  The patterns consist of graceful combinations of curved lines and spirals.  Many other rooms, including the circular chamber, were originally painted with designs in red, which have now almost wholly disappeared.

Many of the chambers are extremely small, too small for an adult even to stand upright in them, and their entrances are merely windows, perhaps a foot square and well above the ground.

What then was the purpose of this wonderful complex of rooms?  Before attempting to answer this question we must consider what has been found in them.  When the museum authorities first took over the hypogeum practically all the chambers were filled to within a short distance of their roofs with a mass of reddish soil, which proved to contain the remains of thousands of human skeletons.  In other words, Halsaflieni was used as a burial place, though this may not have been its original purpose.  The bones lay for the most part in disorder, and so thickly that in a space of about 4 cubic yards lay the remains of no less than 120 individuals.  One skeleton, however, was found intact, lying on the right side in the crouched position, i.e. with arms and knees bent up.

With the bones were found enormous quantities of pottery and other objects, buried with the dead as provision for the next world.  The pottery is rough in comparison with the fine painted wares of Crete, but it is extremely varied in its decoration.  One particularly fine bowl shows a series of animals which have been identified by Professor Tagliaferro as the long-horned buffalo, an animal which once existed on the northern coasts of Africa.  Ornaments of all kinds were common, and include beads, pendants, and conical buttons of stone and shell.  The most remarkable of all are a large number of model celts made of jadeite and other hard stones.  These are of the same shape as the stone axes used by neolithic man, but they are far too small ever to have been used, and they must therefore have been models hung round the neck as amulets.  Each is provided with a small hole for this purpose.  The popularity of the axe-amulet makes it probable that the axe had some religious significance.