OBJECTIVES: The aim of this study was to investigate the long-term outcome after acute high- and intermediate-risk pulmonary embolism (PE) treated with surgical embolectomy or thrombolysis. METHODS: Prospective follow-up including assessment of 30-day and 5-year mortality. Clinical evaluation including ventilation/perfusion scintigraphy by single-photon emission computed tomography in combination with X-ray computed tomography, measurement of pulmonary diffusion impairment, spirometry and echocardiography. RESULTS: A total of 136 patients (64 with high-risk and 72 with intermediate-risk PE) were included, 80 participated in the clinical followup, 16 were alive but declined follow-up and 40 were deceased. For high-risk PE patients the median time to clinical follow-up was 31 months [8-133]. No significant difference was observed in 30-day (P_log-rank = 0.16) or 5-year (P_log-rank = 0.53) mortality between patients treated with surgical embolectomy or thrombolysis. Ventilation/perfusion mismatch identified residual emboli in 4 patients (31%) treated with surgical embolectomy compared to 16 (76%) treated with thrombolysis (P = 0.009). Pulmonary diffusion impairment was identified in 4 patients (31%) treated with surgical embolectomy in comparison to 15 (71%) treated with thrombolysis (P=0.02). In intermediate-risk PE patients, no significant difference in mortality (P_log-rank = 0.51 and 0.86), diffusion impairment or ventilation/perfusion mismatch was found between patients treated with surgical embolectomy or thrombolysis. CONCLUSIONS: Surgical embolectomy for acute high-risk PE has similar mortality, but better outcome on pulmonary end-points when compared to thrombolysis. Patients with high-risk PE could benefit from being referred to a centre with both specialized cardiology and cardiothoracic surgery for interdisciplinary evaluation of optimal treatment strategy.