Objective To compare the effects on biomechanics (?) hemodynamics and plasma levels of brain natriuretic peptide (BNP) when pacing in right ventricular septum and in right ventricular apex. Method Sixty-eight patients performed with DDD pacing, of whom forty-eight with sick sinous syndrome(SSS)and twenty with completely atrioventricularblock, were grouped randomly into two terms according to the site where the ventricular pacing lead fixed. Group one received right ventricular septum(RVS)pacing while the other group received right ventricular apex (RVA) pacing. The QRS waves of the ECG, the left ventricular ejection fraction (LVEF), the cardiac index (CI), the stroke volume (SV) and plasma levels of brain natriuretic peptide (BNP) were compared before and after operations. Patients with SSS in the two groups were programmed and modified three months after operation. Their hemodynamics parameters and plasma levels of BNP were recorded and analyzed in the next three months. Result The QRS duration of lead II of RVA group was longer than RVS group dramatically (P<0.05).There were no obvious differences on LVEF, CI, SV and plasma levels of BNP among the two groups before operation. Compared the hemodynamics and plasma levels of BNP with those in RVS group, the LVEF, CI and SV in RVA group all decreased significantly (P<0.05) three months after operation, but the plasma levels of BNP increased notably (P<0.01). To compare the same parameters for patients with SSS in RVA groups, the LVEF, Cl and SV three months after programming and optimization also increased remarkably(P<0.05), while the plasma levels of BNP decreased obviously (P<0.01), but still higher than those of preoperation evidently (P<0.05). To those patients with SSS in RVS group, there were no difference on LVEF, CI and SV three months after programming and optimization (0.05), however, the plasma levels of BNP decreased remarkably (P<0.05), but there were no difference when compared with those before preoperation (P>0.05). Conclusion The IRVA pacing disturbs the biventricular electrical synchrony and results in the deterioration of the hemodynamics, while the RVS pacing could farthest keep the normal sequence of electrical activity and the synchronous contraction and has no negative effect on the hemodynamics. The RVS pacing shows more physiological better than the RVA pacing.