The purpose of this study is to compare sensitivity and specificity of helical CT and MR imaging for detecting acute pulmonary embolism(PE). Patients who were suspected clinically of having PE were randomly assigned to undergo either helical contrast-enhanced CT or gradient-echo MR (if one modality was contraindicated, the patient was assigned to the other.) Patients were considered to have PE if they had: 1) high-probability V-Q scan and low clinical probability of PE; 2) pulmonary angiogram positive for PE. Patients were considered not to have PE if they had either:1)normal V-Q scan; 2) low probability V-Q scan and low clinical probability of PE; or 3) pulmonary angiogram negative for PE. The CT and MR images were read randomly and independently by five radiologists with varying levels of CT and MR experience. Twenty eight patients underwent CT and 25 MR. A total of 21 patients underwent pulmonary angiography (6 had PE, 15 did not have PE). Of the other 32 patients, 15 had high probability scan/high clinical probability and 17 had low probability scan/low clinical probability. For the five observers, the average sensitivity of CT was 75% and of MR 46%; the average specificity of CT was 89% and of MR 90%. Experience with vascular MR and enhanced CT influenced diagnostic accuracy. For the two vascular MR experts, average sensitivity and specificity of MR were 71% and 97%, and of CT 73% and 97%. In this pilot study, when CT and MR were interpreted with comparable expertise, they had similar accuracy for detecting pulmonary embolism.