Introduction: Right ventricular (RV) pacing causes changes in the heart’s electrical and mechanical activation patterns. QRS duration is a useful surrogate marker of electrical dyssynchrony; longer QRS duration during RV pacing indicates poor prognosis. However, the mechanisms underlying longer QRS duration during RV pacing remain unclear; hence, we investigated factors predicting QRS prolongation during RV pacing. Methods and Results: We enrolled 211 patients who underwent catheter ablation for supraventricular tachyarrhythmia and showed no bundle-branch-block. Three-dimensional mapping for QRS duration during RV pacing from the RV outflow to RV apex was performed, and the difference in QRS duration was analyzed. The predisposing factors causing QRS >160 ms during RV apical pacing were also analyzed. QRS durations at baseline and during RV pacing from the RV outflow and at RV apex were 85.0±7.5 ms, 163.7±17.1 ms, and 156.2±16.1 ms, respectively. With respect to QRS duration, there was a significant correlation between RV outflow and RV apical pacing (r=0.658, p<0.001). The difference in QRS duration between RV outflow and apex in each patient was only 12.5±10.4 ms. Logistic multivariable regression analysis identified baseline QRS duration [odds ratio (OR) 1.24, 95% confidence interval (CI) 1.15 to 1.33, p<0.01], interventricular septum thickness (OR 1.20, 95% CI 1.02-1.40, p=0.025), left atrial diameter (OR 1.08, 95% CI 1.01-1.16, p=0.024), and E/e’ (OR 1.23, 95% CI 1.12-1.35, p<0.01) as significant predictors of prolonged QRS duration during RV apical pacing. Conclusion: QRS duration during RV pacing largely depends not on the pacing site, but on underlying structural heart diseases.