Background Patients with combined aortopulmonary window (APW) and interrupted aortic arch (IAA) malformations are rarely seen. We reviewed cases with such association with emphasis on surgical management and long-term outcome. Methods 109 patients with IAA and 25 patients with APW were operated upon between 1981 and 2011. The clinical records, operation and follow-up data were analyzed. Long-term outcome was completed with the help of either outpatient data or inquiring. Related literature was investigated. Results Combined APW/IAA was found in 8 cases: 7.3% (8/109) of those with IAA diagnosis and 32% (8/25) with APW. All APWs were proximal. 7 patients had interruption type A. A ventricular septal defect (VSD) was associated in one case only. Median age at surgery was 10 days. The two first patients were operated upon without cardiopulmonary bypass (CPB) and one died during operation. The other six underwent single stage approach under CPB with no death: overall early mortality of 12.5% (1/8). APW was closed with one or two patches; aortic arch was reconstructed either directly (extended end-to-side anastomosis) or by patch augmentation. There was no late death and no reoperation during mean follow-up of 118 months (range 1-360 months). Six patients were in functional NYHA class I, the remainder in class II. The cumulative APW/IAA incidence from literature varies between 4.9% (56/1105) and 22.2% (42/189). Early mortality reaches 15.1% (8/53) (95% CI: 6.8% - 27.6%). Conclusion Neonatal repair with thorough mobilization of the aortic arch and extended end-to-side anastomosis or use of patch augmentation carries potential for the best early and late outcome for combined APW/IAA malformation.