Background: Long-term right ventricular apical (RVA) pacing increases the risk of heart failure (HF) by inducing ventricular dyssynchronization. Although recent studies suggest that right ventricular septal (RVS) pacing results in improved short-term outcomes, its long-term effectiveness remains unclear. Methods and results: This study investigated 149 consecutive patients who underwent implantation of a dual chamber pacemaker for atrioventricular block with either RVS-pacing between July 2007 and June 2010 or RVA-pacing between January 2003 and June 2007. The endpoint was defined as death and hospitalization due to heart failure (HF). The rates of mortality and hospitalization due to HF were significantly lower in the RVS-pacing group than that in the RVA-pacing group (event free RVS: 1 year, 98% and 2 years, 98%; RVA: 1 year, 85% and 2 years, 81%; p<0.05). None of the patients died from HF in the RVS-pacing group, while 4 patients died from HF in the RVA-pacing group within 2 years after pacemaker implantation. The paced QRS interval was significantly shorter with RVS pacing than with RVA pacing at different times after pacemaker implantation (RVS: immediately 157.8±24.0 ms, after 3 months 157.3±17.5 ms, after 6 months 153.6±21.7 ms, after 12 months 153.6±19.4 ms, after 24 months 149.3±24.0 ms vs. RVA: immediately 168.3±23.7 ms, after 3 months 168.7±26.0 ms, after 6 months 168.0±22.8 ms, after 12 months 171.2±22.3 ms, after 24 months 176.1±25.5 ms; p<0.05). Conclusions: RVS pacing is feasible and safe with more favorable clinical benefits than RVA pacing.