Congenital choanal atresia is a rare malformation of the upper airways occurring sole or within the scope of syndromes. The controversy regarding standardized surgical approach and optimal technique preventing re-stenosis as well as the proceeding in case of a unilateral malformation persists. To address these issues, a retrospective analysis of patients presenting with choanal atresia in our department within the last 10 years was performed. 15 infants aged 3 days to 13 years (mean 42 months) who presented with unilateral (10 cases) and bilateral (5 cases) choanal atresia underwent surgical repair. 4 patients failed previous surgeries. All interventions were performed in transnasal endoscopic technique. 7 patients were intraoperatively stented for 6 weeks, 4 patients for 1 week. In 73% (11 out of 15 children) further congenital anomalies were identified. In 7 cases a re-stenosis requiring treatment occurred, predominantly in long-term stented patients. No intra- or postoperative hemorrhages or infections occurred. To provide an adequate work-up of affected patient including a screening for further congenital anomalies, a multidisciplinary approach is required. Endonasal endoscopic approach represents a safe technique for surgical repair of choanal atresia. The indication for surgical repair in case of a unilateral atresia is based on the severity of clinical symptoms. The use of stents, especially of long term, remains controversial and needs further evaluation.