The aim of this study is to report our experience in surgical treatment of unilateral and bilateral choanal atresia. We describe the endoscopic surgical technique for creation of neochoanes and following repeating balloon dilation after surgery to stabilise the results. The study was carried out from December 2014 to December 2018, enrolling 46 patients who underwent surgery for choanal atresia at the Otolaryngology Unit of the Paediatric hospital Bambino Gesù: 17 with bilateral choanal atresia (Group A) and 29 with unilateral choanal atresia (Group B). All patients underwent transnasal endoscopic surgery. The incision of the mucosa was made with a cold and hot system (laser diode). The elimination of atresic plaque was possible thanks to the use of a drill; the calibration of the neo-choanes was carried out with the help of balloon dilation. No stent was used, and no patient underwent treatment with topical mitomycin. The first endoscopic follow-up was made 7 days after surgery with surgical curettage and a second balloon dilation 15 days after surgery to stabilise the new choanes. Further check-ups were suggested at 1 month after surgery and later based on individual progress. In group A, the average age for the first treatment was 10.4 days, and atresia was associated with other anomalies in 64% of cases. The therapeutic protocol led to a successful outcome in 82% of cases, with an average of 4.6 procedures per patient (range: 3-11). In group B, the average age for the first treatment was 36.6 months, association with other anomalies was 27% of cases and the prevalent side was the right (11:6).