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Infective endocarditis (IE) is a rare entity in children and predominantly affects patients with congenital heart defects (CHD). Our study assesses the association between the time to diagnosis of IE and the time to surgery and outcome. The mean period from initial symptom presentation to diagnosis confirmation was 38 days (3-180 days). 12 patients (60%) had an early diagnosis (< 30 days), while in 8 cases (40%) the diagnosis was delayed (>30 days). 75% of the patients with a delayed diagnosis had received prior antibiotic therapy vs. 58% of the children with an early diagnosis. All 3 children with lethal outcomes had received prior antibiotic therapy, in two of the cases the diagnosis of IE was early, and in one case it was delayed. In conclusion, empiric antibiotic therapy is associated with a delayed diagnosis of infective endocarditis, and the longer the time to surgery the greater the risk for unfavorable patient outcome.