The aim was to investigate the effect of balloon pulmonary angioplasty (BPA) on right ventricular (RV) function in chronic thromboembolic pulmonary hypertension. Twenty-six patients with chronic thromboembolic pulmonary hypertension were enrolled and were divided into 2 groups, group H with high (>30 mm Hg) mean pulmonary arterial pressure and group L with low (25 to 30 mm Hg) mean pulmonary arterial pressure. RV function was assessed using 2-dimensional speckle-tracking echocardiography as well as 3-dimensional echocardiography, and RV dyssynchrony was assessed by the RV strain curves. Exercise capacity was evaluated by the 6-minute walk distance. RV dilatation was significantly reduced after BPA. In group H, RV ejection fraction, RV free wall longitudinal strain and RV dyssynchrony were all impaired before BPA and were ameliorated after BPA. In group L, RV ejection fraction as well as RV dyssynchrony were impaired without the reduction of RV free wall longitudinal strain and were improved after BPA, indicating that RV dysfunction may be attributable to the RV dyssynchrony in group L. Furthermore, RV dyssynchrony at baseline was the only parameter that was correlated with improvement in the 6-minute walk distance after BPA. RV dyssynchrony may affect RV function and could be the useful parameter for clinical outcome after BPA.