Functional mitral regurgitation (MR) (FMR) and atrial fibrillation (AF) are common in patients undergoing left ventricular assist device (LVAD) implantation. However, the impact of FMR and AF on clinical outcomes is uncertain. This study aimed to investigate the characteristics and prognostic significance of FMR and AF in patients with LVADs. We retrospectively reviewed all patients who underwent LVAD implantation at our center between January 2010 and December 2017. We defined significant FMR as the ratio of MR color jet area to left atrial area of >20% and persistent or permanent AF (PeAF) as persistent or permanent AF at LVAD implantation. A total of 380 patients were included in this analysis. Patients were divided into 6 groups: patients with no PeAF and no significant FMR (Group 1), patients with no PeAF but with significant FMR (Group 2), patients with PeAF but no significant FMR (Group 3), patients with PeAF and significant FMR (Group 4), patients with concomitant mitral valve surgery (MVS) at LVAD implantation and without PeAF (Group 5), and patients with concomitant MVS and with PeAF (Group 6). A total of 56 patients (15%) died within 2 years. Kaplan-Meier curve analysis demonstrated a 2-year survival of 81% in Group 1, 89% in Group 2, 87% in Group 3, 47% in Group 4, 87% in Group 5, and 79 % in Group 6 (log-rank test, p < 0.001). The multivariable Cox proportional-hazards model showed that classification in Group 4 was an independent predictor of mortality (hazard ratio, 4.31; 95% CI: 2.19-8.46; p < 0.001). The coexistence of significant FMR and PeAF may represent a poor prognostic marker in patients undergoing LVAD implantation.