We present the first application of cross-dating (Th/U measured by thermo-ionization mass spectrometry (TIMS) and 14C measured by accelerator mass spectrometry (AMS)) of calcite covering prehistoric paintings. Th/U age estimates of cave drapery range from 9800 to 27,300 yr B.P. while conventional 14C age is estimated between 9900 and 7610 yr B.P. depending on the dead carbon correction. The age discrepancy is attributed to a disturbance of Th/U and/or 14C geochemical systems, showing the limits of the geochronological approach applied to this kind of material. For the Th/U system, the poor consistency of U data (U content, 234U/238U activity ratios) and apparent ages argue for open system conditions. For 14C system, variation of the dead carbon fraction (dcf) and a possible mixing of successive generations of calcite could account for age discrepancy. Nevertheless, one sample shows concordant ages for the two methods. Compatible ages through corrections for open system conditions are assumed for other samples. Then, the cross-dating suggests 9900 yr as the minimum age of the piece of drapery; the underlying painting must be older. This study of rock art demonstrates the presence of a Pleistocene population before 9900 yr in the southeast of Borneo, whereas previously the only population in evidence in this area was of Austronesian type from ∼5000 to 6000 yrs ago.