Surgery is indicated in about 50% of infective endocarditis patients, and bleeding or the transfusion of blood a common finding. The intraoperative use of cell salvage may reduce the perioperative transfusion requirement, but its use is limited in the underlying disease. In this retrospective study, we therefore evaluated n = 335 patients fulfilling the modified Duke criteria for infective endocarditis characterized by the use of intraoperative cell salvage with autologous blood retransfusion. Inflammation markers and organ dysfunction, including catecholamine dependency, were evaluated by using linear regression analysis. Between 2015 and 2020, 335 patients underwent surgery for left-sided heart valve endocarditis. Intraoperative cell salvage was used in 40.3% of the cases, especially in complex scenarios and reoperation. Intraoperative cell salvage significantly altered the white blood cell count after surgery. On average, leucocytes were 3.0 Gpt/L higher in patients with intraoperative cell salvage compared to patients without after adjustment for confounders (95% CI: 0.39-5.54). Although the difference in WBC was statistically significant, i.e., higher in the ICS group compared to the no-ICS group, this difference may be clinically unimportant. Organ dysfunction, including hemodynamic instability and lactate values, were comparable between groups. In conclusion, intraoperative cell salvage enhanced the re-transfusion of autologous blood, with minor effects on the postoperative course of inflammatory markers, but was not associated with increased hemodynamic instability or organ dysfunction in general. The restriction of intraoperative cell salvage in surgery for infective endocarditis should be re-evaluated, and more prospective data in this topic are needed.