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Objectives Cardiac surgery is a life-saving procedure in patients diagnosed with infective endocarditis (IE). There are several validated risk scores developed to predict early-mortality; nevertheless, long-term survival has been less investigated. The aim of the present study is to analyze the impact of IE-specific risk factors for early and long-term mortality. Methods An observational retrospective study was conducted that included all patients who underwent surgery for IE from 2002 to 2016. Median follow-up time after surgery was 53.2 months (IQI 26.2–106.8 months). In-hospital mortality was analyzed using multiple logistic regression. Long-term survival was analyzed after one, two and five years. Cox proportional hazards regression was employed to identify risk factors related to long-term mortality. Results Of the 180 patients underwent cardiac surgery, 133 were discharged alive (in-hospital mortality was 26.11%). 6 variables were identified as independent factors associated with in-hospital mortality, most of them closely related to the severity of IE: age, multivalvular involvement, critical preoperative status, preoperative mechanical ventilation, abscess and thrombocytopenia. Long-term survival in patients discharged alive was 89.1%, 87.4% and 77.6% after one, two and five years. Long-term mortality was independent of specific IE factors and 86.51% of deaths were not related to cardiovascular or infectious diseases. Conclusion Despite the high perioperative mortality rate after surgical treatment for active IE, long-term survival after hospital discharge was acceptable, regardless of the severity of the endocarditis episode. Although in-hospital survival depended mainly on several IE factors, long-term survival was not related to the severity of endocarditis baseline affection.