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Background: The prognostic impact of residual vegetation (RV) after medical treatment for endocarditis remains unknown. Methods: 134 consecutive patients hospitalized for infective endocarditis, not surgically treated, with the presence of vegetation at diagnosis, were included retrospectively. The follow-up started at the end of antibiotic treatment when healing was complete. The presence or absence of RV was assessed at this time. The primary endpoint was a composite of the occurrence of embolic events, recurrence of endocarditis, or death from any cause. Results: Eighty-five patients were men (63%), mean age was 69 ± 15 years, and median follow-up was 16.3 (IQR: 5–30) months. Sixty-six patients (49%) had RV, 15 (11%) had RV > 10 mm and nine (7%) had RV with an increase in size relative to that of the diagnosis. The primary endpoint occurred in 23 patients (35%) in the group with RV, and in 16 patients (24%) without RV, which was not statistically relevant (HR 1.70; 95% confidence interval (CI) 0.89–3.22; p = 0.10). Based on univariate Cox regression analysis, the occurrence of the primary endpoint was associated with RV that increased (HR 3.90 95% CI 1.61–9.43; p < 0.01), RV size (HR 1.05; 95% CI 1.01–1.09; p < 0.01) or RV > 10 mm (HR 3.35; 95% CI 1.51–7.39; p < 0.01). Only RV > 10 mm remained significant in multivariate Cox regression: HR3.29; 95% CI 1.20–8.96; p = 0.02. Conclusions: RV is frequent but has no clear prognostic impact in itself; however, its size, particularly in comparison with the start-of-treatment data, merits particular attention as being potentially associated with increased risk.