Objective: To compare the clinical and epidemiological features, treatments, and outcomes of patients with isolated right-sided and left-sided fungal endocarditis and to determine the risk factors for in-hospital mortality in patients with Candida sp endocarditis. Methods: A retrospective review of all consecutive cases of fungal endocarditis from five hospitals was performed. Clinical features were compared between patients with isolated right-sided and left-sided endocarditis. In the subgroup of fungal endocarditis due to Candida species, binary logistic regression analysis was performed to determine variables related to in-hospital mortality. Results: Seventy-eight patients with fungal endocarditis were studied. Their median age was 50 years; 55% were male and 19 patients (24%) had isolated right-sided endocarditis. Overall, cardiac surgery was performed in 46 patients (59%), and in-hospital mortality was 54%. Compared to patients with left-side fungal endocarditis, patients with isolated right-sided endocarditis had lower mortality (32% vs. 61%; p = 0.025) and were less often submitted to cardiac surgery (37% vs. 66%; p = 0.024). The most frequent etiology was Candida spp (85%). In this subgroup, acute heart failure (odds ratio 5.0; p = 0.027) and exclusive medical treatment (odds ratio 11.1; p = 0.004) were independent predictors of in-hospital death, whereas isolated right-sided endocarditis was related to a lower risk of mortality (odds ratio 0.13; p = 0.023). Conclusions: Patients with isolated right-sided fungal endocarditis have particular clinical and epidemiological features. They were submitted to cardiac surgery less often and had better survival than patients with left-sided fungal endocarditis. Isolated right-sided endocarditis was also a marker of a less harmful illness in the subgroup of Candida sp endocarditis.