Abstract Introduction Despite modern diagnostics, targeted antibiotic therapy and surgical treatment the mortality rate of infective endocarditis (IE) remains high. In developed countries both the risk factors and pathogens have changed. Objective and methods In our retrospective study we analyzed the clinical and microbiological characteristics, short- and long-term all-cause mortality, and temporal trends of consecutive patients admitted with IE between 2006 and 2018. Results We included 537 cases in our study, the mean age was 55.9 ± 16.5 years (72.2% male). 325 (60.5%) cases were native left-sided IE, 14 (3%) cases were right-sided IE, 130 (24%) cases were prosthetic valve IE, 62 (11.5%) cases were intracardiac device-related IE and 6 (1%) other cases. The most common microorganisms were Staphylococci (n=175; 33%), including 104 cases of methicillin-sensitive Staphylococcus aureus (MSSA), 27 cases of methicillin-resistant Staphylococcus aureus (MRSA) and 44 cases of coagulase-negative Staphylococci. Streptococcus species were identified in 141 cases (26%), Enterococcus species in 88 cases (16%) and 72 cases (13%) were classified as blood culture-negative IE. In-hospital all-cause mortality was 14%, mortality at six months was 27%, at one-year was 31%, and at five-year was 45%. The incidence of MSSA infections increased over time (p=0.024), while coagulase-negative Staphylococci (p<0.001), and Streptococci (p=0.047) infections decreased. None of the observed mortality rates showed significant change over the study period. Predictors of mortality were advanced age (HR 1.37; p<0.001), impaired renal function (HR: 1.03; p<0.001), reduced ejection fraction on admission (HR 1.38; p<0.001), stroke (HR 1.74; p=0.001), and MRSA infection compared to Streptococci (HR 2.56; p=0.002). Conclusion During the observed 13-year period Staphylococci were the most common pathogens, with an increasing incidence of MSSA infection in our tertiary center. The mortality rate of IE remained high and showed no improvement over time.