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Background and objectives Right ventricular apical (RVA) pacing has been reported impairing left ventricular (LV)performance. Alternative pacing sites in right ventricle (RV) has been explored to obtain better cardiac function. Our study was designed to compare the hemodynamic effects of right ventricular septal (RVS) pacing with RVA pacing. Methods Ten elderly patients with chronic atrial fibrillation (AF) and long RR interval or slow ventricular response (VR) received VVI pacing. The hemodynamic difference between RVS and RVA pacing were examined by transthoracic echocardiography (TTE). Results Pacing leads were implanted successfully at the RVA and then RVS in all patients without complication. The left ventricular (LV) parameters,measured during RVA pacing including left ventricular ejection fraction (LVEF), FS, stroke volume (SV) and peak E wave velocity (EV) were decreased significantly compared to baseline data, while during RVS pacing, they were significantly better than those during RVA pacing. However, after 3-6 weeks there was no statistical significant difference between pre- and post- RVS pacing.Conclusions The LV hemodynamic parameters during RVA pacing were significantly worse than baseline data. The short term LV hemodynamic parameters of RVS pacing were significantly better than those of RVA pacing; RVS pacing could improve the hemodynamic effect through maintaining normal ventricular activation sequence and biventricular contraction synchrony in patients with chronic AF and slow ventricular response.