D-dimer blood tests have been suggested to rule out pulmonary embolism. Despite evidence of the safety of withholding anticoagulant treatment in patients with suspected pulmonary embolism and a normal D-dimer assay result, clinicians remain reluctant to use a D-dimer assay as a sole diagnostic test. This prospective study in 314 consecutive inpatients and outpatients investigates the relation between the diagnostic accuracy of D-dimer plasma concentration and pulmonary embolus location. Plasma D-dimer levels were measured using a quantitative immunoturbidimetric method. A strict protocol of ventilation-perfusion scintigraphy, pulmonary angiography, and spiral computed tomography was used to arrive at a final diagnosis and to assess the largest pulmonary artery in which embolus was visible. The influence of embolus location on the diagnostic accuracy was evaluated using the Kruskal-Wallis test and receiver operator characteristics (ROC) analysis. There was a strong correlation between plasma D-dimer concentration and embolus location (Kruskal-Wallis, p < 0.001). Thus, the assay showed greater accuracy in excluding segmental or larger emboli (sensitivity = 93%) than subsegmental emboli (sensitivity = 50%). D-dimer concentration and the accuracy of D-dimer assays are clearly dependent on embolus location and smaller, subsegmental emboli may be missed when D-dimer assays are used as a sole test to exclude pulmonary embolism.