Abstract The giant oil fields of the Val D’Agri region (Southern Apennines Internal Thrust Zone, Italy) may rank as the largest onshore accumulations in Europe, but these resources pose special technical challenges due to the secondary alteration process identified as compositional grading. This alteration process is attributed to petroleum system elements and processes that lead to the formation of an unstable oil column. These oil columns are studied within a mass balance perspective that allow identification of key molecular fractionations which can be used to properly diagnose this alteration mechanism in other oil accumulations. The molecular signature is defined in the organic sulphur fraction as well as different hydrocarbon classes, and is completely consistent with the engineering criteria for this reservoir process. This discovery is particularly critical to reservoir compartment studies as the failure to recognize this particular signal will invariably lead to the identification of false compartments.