Objective To evaluate the influence of right ventricular outflow tract septal ( RVS) pacing with right ventricular apical ( RVA) pacing on left ventricular remodeling and brain natriuretic peptide ( BNP). Methods Sixty patients with indication of pacemaker implantation were randomized into two groups, RVA group and RVS group. BNP was measured with ELISA, and echocardiography was performed to measure the left ventricular end diastolic volume ( LVEDD), left ventricular end systolic volume ( LVEDV) and left ventricular ejection fraction (LVEF) at pre-operation,and after 6,12,24 months pacing. The difference of cardiac remodeling and BNP in the two groups was observed. Results Compared to BNP at pre-operation (( 60. 2 ± 15. 7 ) ng/L) , BNP increased significantly in the RVA group at the 6th,12th and 24th month after operation( ( 108. 2 ±29. 8) , ( 190. 3 ±46. 7) ,(308. 2 ±56. 5)ng/L,respectively) (P <0. 05). In the RVS group,BNP increased only at 24 months after pacing ( (75. 2 ± 15. 8) ng/L vs. (63. 9 ± 15. 1 ) ng/L) (P < 0. 05). There was significant difference on BNP between the two groups. LVEDD,LVEDV increased,LVEF declined at 12 months after pacing in the RVA group,which were not observed in the RVS group. There was significant difference on LVEDD,LVEDV and LVEF in the RVA group (P< 0. 05) between the 12th month and pre-operation,and there were no significant difference in the RVS group (P > 0. 05). Conclusions Compared to RVA pacing,RVS pacing was more beneficial to improve heart function,prevent cardiac remodeling and decline the activation of nerve-endocrine.