Abstract: AIM To observe the clinical efficacy of targeted therapy for patients with Eisenmenger syndrome (ES). METHODS A total of 36 ES patients aged 9 to 51 years ［mean (38.6±17.7) years］, among whom 24 were females, were evaluated. Among the patients, 14 had ventricular septal defect (VSD), 11 had atrial septal defect (ASD), six had patent ductus arteriosus (PDA), three had VSD+PDA, and two had ASD+PDA. According to the treatment regimens, patients treated with bosentan or sildenafil were divided into long-term therapy group (regular medication for 2 years) and intermittent therapy group (cumulative medication for 6 months). Efficacy of the therapy was evaluated after the 2-year treatment. RESULTS Compared with those pre-treatment, SpO2 and the 6-min walking test (6MWT) distance in the long-term therapy group increased significantly (P<0.05). Borg score, NYHA-FC, BNP and sPAP decreased obviously (P<0.05) after treatment. Compared with those pre-treatment, Qp/Qs in the long-term therapy group increased significantly (P<0.05), and mPAP and Pp/Ps decreased obviously (P<0.05). PVR also decreased but showed no significant difference. Compared with those pre-treatment, SpO2 and 6MWT distance in intermittent therapy group increased (P<0.05). BNP decreased obviously (P<0.05). Borg score and NYHA-FC and sPAP also decreased but showed no significant difference. Although no significant difference was found in the 6MWT distance, Borg score, NYHA-FC, BNP and sPAP between groups, SpO2 in long-term therapy group increased obviously (P<0.05). CONCLUSION Intermittent targeted therapy could partially benefit patients with ES.