Background The prognosis of patients with suspected pulmonary embolism (PE) in whom PE has been ruled out (RPE) is unclear. We aimed to evaluate survival and diagnosis of new cancer in suspected PE patients at follow up. Methods A prospective cohort study nested in a prospective Institutional Registry of Venous Thromboembolic Disease was performed between 2006 and 2011. This study was designed to evaluate all consecutive, incident cases of suspected PE in adults. The study was performed at the Hospital Italiano de Buenos Aires, a tertiary level hospital, in hospitalized patients and outpatients. Suspected PE cases were collected using a computerized system that alerts whenever a physician requests pulmonary angiography, angiotomography, or ventilation-perfusion scintigraphy. PE was defined by pre-specified criteria and RPE was defined when diagnostic tests were negative for PE. Results We included 1736 cases of suspected PE. The prevalence of PE was 29% (n = 504). There was no difference in the overall survival at 30 days and follow-up between PE and RPE patients. The presence of provoked or unprovoked venous thromboembolic disease in these patients did not affect survival. The main causes of death were PE in the confirmed PE group (60%), and neoplasm (42%) and sepsis (37%) in the RPE group. Survival at 90 days was 63% for PE (95% CI 58–67%) and 67% for RPE patients (95% CT 64–69%). At follow-up, there was no difference in diagnosis of new cancer between PE and RPE patients (2% vs 2%, p = 0.82), even when taking into account the unprovoked group. Conclusions Even when the main cause of death in PE patients is PE itself, the overall mortality is similar between PE and RPE patients. The reason for this finding could be because of the more frequent and severe comorbidities in RPE than in PE patients. Trial registration HomeClinicalTrial.gov: NCT01372514