Right ventricular (RV) septal pacing has been advocated as an alternative to apical pacing to avoid long-term detrimental effects. There is conflicting evidence on the benefits of RV septal pacing. Fifty-five subjects (22 normal healthy controls, 17 with RV septal pacing, and 17 with apical pacing) were recruited. Midventricular short-axis left ventricular (LV) circumferential and radial strains were determined. Circumferential and radial strain dyssynchrony and longitudinal systolic dyssynchrony were determined. Echocardiographic determination of pacing sites were compared with electrocardiogram and chest x-ray. Septal pacing is a heterogenous group of different pacing sites, and there was only modest agreement among echocardiogram, electrocardiogram, and chest x-ray. Median pacing durations were 436 days for septal pacing and 2,398 days for apical pacing. Mean QRS duration for apical pacing was longest, followed by septal pacing and control (p <0.001). LV mass index, end-systolic volume index, and ejection fraction were more impaired in septal than in apical pacing (all p values <0.05). Septal pacing was associated with more impaired circumferential strain (p <0.001) and worse LV dyssynchrony than apical pacing and control. In conclusion, standard fluoroscopic and electrocardiographic implantation techniques for RV septal pacing resulted in a heterogenous group of different pacing sites. This heterogenous RV septal pacing group was associated with poorer long-term LV function and greater dyssynchrony than RV apical pacing and control.