Agnes was buried in a preexisting hypogeum cemetery, that – according to ancient sources – was owned by the family of the martyr and located close to an imperial property.
The epigraphic sources and the kind of sepulture allow to gather that the cemetery dates back the second half of 3rd century and corresponds to the first region of the whole subterranean complex.
It was later studied by Antonio Bosio in its Roma sotterranea ("Subterranean Rome"; 1632), although the author mixed it up with the nearby Coemeterium maius ("Greater Catacomb").
On behalf of Giovanni Battista de Rossi, in the second half of 19th century Mariano Armellini made a series of excavations into the hypogeum cemetery, recovering some parts in good preservation status.
At the beginning of the 20th century, the priest Augusto Bacci, on behalf of the titular cardinal of the basilica, carried out some excavations, which were fundamental for the historical and topographic restoration of the memory of St. Agnes and the first region.