Abstract Background Patients with end-stage renal disease (ESRD), particularly those undergoing dialysis, have a significantly higher risk of developing infective endocarditis (IE) compared to the general population. ESRD is not only related to a higher risk of infection, but also to a worse prognosis in IE. However, most data regarding the epidemiology and outcomes of patients with ESRD and IE is derived from noncontemporary population-based studies with limited clinical variables and lack of complete microbiological information, or from retrospective single-center cohorts. Purpose The aim is to describe the clinical characteristics and outcome of patients with IE and ESRD in Spain, compared to patients without ESRD, and to investigate potential differences between patients undergoing dialysis and the rest of patients with ESRD. Methods Retrospective observational population-based study. A total of 9,008 episodes of IE between 2016 and 2019 were analysed using information from the Spanish Minimum Basic DataSet. 428 patients had ESRD, of whom 332 were undergoing dialysis. A multivariable and multilevel logistic model was developed to evaluate the association of different variables with in-hospital mortality in ESRD patients. Results Compared to patients without ESRD, those with ESRD were younger, had more comorbidities, and had a higher incidence of Staphylococcus aureus (31.8% vs. 18.4%; p <0.001) and coagulase-negative staphylococci infections (19.2% vs. 14%; p =0.006). In terms of in-hospital complications, septic shock was more frequent in patients with ESRD (12.1% vs. 8.9%; p=0.007). Furthermore, ESRD patients underwent cardiac surgery less frequently than patients without ESRD (12.6% vs. 19.6%; p <0.001) and had significantly higher in-hospital mortality (33.4% vs. 26.9%; p =0.003). When comparing patients undergoing dialysis with the rest of ESRD patients, it was observed that those on dialysis had more comorbidities and a higher proportion of Staphylococcus aureus infections (36.1% vs. 16.7%; p <0.001). No differences were found in observed in-hospital mortality between patients on dialysis and the rest of ESRD patients. The multilevel analysis revealed that dialysis was not an independent risk factor for in-hospital mortality in patients with ESRD. Cardiac surgery was also not independently associated with higher in-mortality in ESRD patients. Conclusions Patients with ESRD and IE have a different clinical and microbiological profile than other patients with IE. Moreover, they undergo cardiac surgery less frequently and have significantly higher in-hospital mortality. Dialysis treatment and cardiac surgery were not independent risk factors for mortality in ESRD patients with IE.