The scoring system most commonly used to date to describe the thrombotic burden of deep vein thrombosis (DVT) excludes several deep vein segments and is thereby of limited use in research. The aim of this prospective, comparative study was to develop a new scoring and distribution system that would include all major deep veins of the leg and pelvis. In total, 247 consecutive patients were included, of whom 105 had a positive phlebography. The positive phlebographies were registered in the new system and the result was compared with that obtained by the Marder system. In 72% (76/105) of the patients the DVT distribution was not completely described and the thrombotic burden was significantly underestimated by the Marder system. Of these, 12% (13/105) were not scored at all, thus representing false-negative investigations. It was possible to score all DVTs and important vein segments of these patients with the new system. The scoring system previously used excludes several deep vein segments. A description of the important vein segments, where DVT is shown to originate and propagate, is mandatory in a scoring system designed for the purpose of research of DVT and later detected deep vein insufficiency. The new system meets this demand.