This study prospectively evaluates whether a previously established adverse outcome score (the Geneva prognostic score) predicts 3 and 12-month overall mortality among the patients diagnosed with pulmonary embolism (PE) by a CT pulmonary angiogram (CTPA). Five hundred twenty-three consecutive patients who had CTPA for suspected PE were recruited prospectively from March 2003 to October 2004. The Geneva prognostic score was calculated for all patients. Twelve-month follow up was completed in all patients in December 2005. There were 105 patients diagnosed with PE. The mean score was 2.71 (standard deviation (SD) 1.25) for those patients who had died (n = 7) and 1.14 (SD 1.19) for those patients who were alive (n = 98) at 3-month follow up (P < 0.001). The mean scores were 2.69 (SD 0.95) for those who had died (n = 13) and 1.04 (SD 1.15) for those patients who were alive (n = 92) at 12-month follow up (P < 0.001). At 3-month follow up, among the 88 patients with a score of 2 or less, three patients (3.4%) died and among 17 patients with a score of greater than 2, four patients (23.5%) died (P = 0.01). At 12-month follow up, five patients (5.7%) with a score of 2 or less died and eight patients (47.1%) with a score of three or more died (P < 0.0001). The Geneva prognostic score stratifies patients with low and high risk for overall mortality at 3 and 12 months among patients diagnosed with PE by CTPA.