Carved into the inner faces of the tomb's upright stones, known as orthostats, are a series of cupmarks, small circular depressions pecked into the rock surface, that only become apparent under particular lighting conditions, when raking or low-angled light catches the shallow relief.

According to research by Gibbons (2007), five and possibly six cupmarks, ranging from roughly one to two and a half centimetres wide and around one to one and a half centimetres deep, are distributed across the interior face of the northern orthostat, with a single further cupmark on the southern one. A possible circular area of lighter pecking has also been identified close to the northern group, though its status as deliberate carving is less certain. One of the cupmarks presents a particular interpretive puzzle: the largest and deepest of the group may have begun as a natural hollow in the stone, subsequently shaped or deepened by human hands. Cupmarks are among the most widespread forms of prehistoric rock art found across Ireland and Britain, their precise meaning or function still debated, but their presence within the chamber of a wedge tomb, a burial monument type associated with the later Neolithic and early Bronze Age, suggests they were not merely decorative afterthoughts.

Visitors to Gleninsheen should bear in mind that the markings are genuinely difficult to see without the right conditions. Early morning or late afternoon light, when the sun is low and strikes the stone at an oblique angle, offers the best chance of making them out. It is worth taking a moment inside the chamber to let your eyes adjust and to look carefully at the stone surfaces rather than the monument's overall form.