Background International guidelines recommend 4 weeks of treatment with ampicillin plus gentamicin (A+G) for uncomplicated native valve Enterococcus faecalis infective endocarditis (EFIE) and 6 weeks in the remaining cases. Ampicillin plus ceftriaxone (A+C) is always recommended for at least 6w, with no available studies assessing its suitability for 4w. We aimed to investigate differences in the outcome of EFIE according to the duration (4 versus 6 weeks) of antibiotic treatment (A+G or A+C). Methods Retrospective analysis from a prospectively collected cohort of 78 EFIE patients treated with either A+G or A+C. Results 32 cases (41%) were treated with A+G (9 for 4w, 28%) and 46 (59%) with A+C (14 for 4w, 30%). No significant differences were found in 1-year mortality according to the type of treatment (31% and 24% in A+G and A+C, respectively; P = 0.646) or duration (26% and 27% at 4 and 6w, respectively; P = 0.863). Relapses were more frequent among survivors treated for 4w than in those treated for 6w (3/18 [17%] at 4w and 1/41 [2%] at 6w; P = 0.045). Three out of 4 (75%) relapses occurred in cirrhotic patients. Conclusions A 4-week course of antibiotic treatment might not be suitable neither for A+G nor A+C for treating uncomplicated native valve EFIE.