Before the Neolithic builders arrived, the knoll was a hunting and tool-making spot for far older people. Excavations between 1977 and 1979 found flint and chert tools and the remains of hearths on the original ground surface beneath the cairn; charcoal from one of those hearths carbon-dated to around 3,100 BCE, give or take 70 years. The pottery in the same layer was undecorated Irish Sea ware - the standard early- and middle-Neolithic ceramic of the western British coast. Most of the clay came from somewhere nearby. One sherd, though, contained a small inclusion of perthitic biotite granite that does not match any local rock; that pot had travelled, probably from Ireland or possibly from Scotland or Cornwall. The pollen preserved in the adjacent peat bog tells a longer story: sub-arctic tundra after the ice retreated, then birch and grass, then full deciduous climax forest of oak, elm and hazel that covered the island before the first farmers began cutting it down.

The first chamber was a simple square box of stone at what is now the western end, originally covered by a circular cairn that may have been a passage grave. It produced very few finds but enough heavily decorated Peterborough ware pottery to suggest it stayed in use for a long time. The second chamber, rectangular and entered through a narrow forecourt marked by two upright stones, was added later; the builders covered both chambers under a single long wedge-shaped cairn edged with drystone walling. Then, later still, the third chamber was added to the front of the central one, with another monumental entrance and another extension of the cairn to cover it - but no longer with access to the original middle chamber, which was now sealed inside the structure. Late Neolithic pottery found at the third entrance suggests this final phase was still receiving offerings into the very end of the period, perhaps around 2,500 BCE. The whole sequence - three monuments in one, built over hundreds of years - is now considered a textbook example of how Neolithic communities in western Britain adapted and reused their sacred places.

By the time John Aubrey visited around 1655 and called the place Y-Lleche (the stones), the cairn had already been heavily disturbed and several of the standing stones had fallen. In about 1790 the situation got much worse: the capstones were levered off and carted away to be reused as gateposts and lintels on nearby farms. Urns and bones were turned up in the process and lost. The monument might have been entirely destroyed if Margaret Stanley, who had inherited the Penrhos estate that included the site, had not intervened. Her grandson William Owen Stanley wrote about her rescue of the tomb in 1867. In 1856, in the spirit of the Celtic Revival, a Victorian visitor stood on the spot and imagined Druid priests in white robes performing human sacrifices on a crimson-stained altar - a wholly fictional projection, but a typical Victorian one. The truth is more interesting and quieter: a small community on Holy Island who buried their dead here in stages over fifteen hundred years, leaving us a structure that has now stood for nearly six thousand. A line of small standing stones extends 350 metres northwest from the tomb, pointing within one degree at the winter solstice sunrise.