In this work, the methods of the Prospective Investigation of Pulmonary Embolism Diagnosis III (PIOPED III) are described in detail. PIOPED III is a multicenter collaborative investigation sponsored by the National Heart, Lung and Blood Institute. The purpose is to determine the accuracy of gadolinium-enhanced magnetic resonance angiography in combination with venous phase magnetic resonance venography for the diagnosis of acute pulmonary embolism (PE). A composite reference standard based on usual diagnostic methods for PE is used. All images will be read by 2 blinded and study-certified central readers. Patients with no PE according to the composite reference test will be randomized to undergo gadolinium-enhanced magnetic resonance angiography in combination with venous phase magnetic resonance venography. This procedure will reduce the proportion of patients with negative tests at no loss in evaluation of sensitivity and specificity.