BACKGROUND: The risk of recurrence of pulmonary embolism (PE) is higher in men than in women. Differences in clinical presentation of deep vein thrombosis (DVT) have been reported between the two genders but comparative data on PE are lacking. OBJECTIVES: To compare clinical characteristics between women and men with suspected and confirmed PE and their impact on clinical probability prediction scores and on diagnostic work-up of PE, and to assess whether differences at presentation could account for the increased recurrence rate in men. METHODS: Combined data from three prospective cohort studies including a total of 3414 outpatients with suspected PE were analyzed retrospectively. Clinical characteristics, pretest probability of PE, diagnostic yield of non-invasive tests and VTE recurrence rate were compared between genders. RESULTS: The overall prevalence of PE was similar among women and men (22.3% vs. 23.1%; P = 0.55). The clinical probability prediction scores (Geneva score and Wells score) performed equally well in both genders. A non-invasive diagnostic work-up was possible more often in men than in women. The proportion of PE-associated proximal DVT was higher in men than in women (43% vs. 33%; P = 0.009). VTE recurrence rate was also higher in men than women with PE (5.0% vs. 2.3%; P = 0.045). CONCLUSION: In spite of some differences in the clinical presentation of PE between women and men, clinical probability prediction scores perform equally in both genders. A higher prevalence of PE-associated proximal DVT in men could possibly indicate greater severity of PE episodes and partly account for the higher VTE recurrence rate in men.