Choanal atresia is a congenital malformation of the posterior portion of the nasal cavity, which is usually unilateral. The incidence is estimated to be 1 in 5,000 to 8,000 live births. Several surgical approaches have been described to correct choanal atresia since Emmert's initial trocar perforation in 1853, including transnasal, transpalatal, transseptal, sublabial transseptal, transantral, and external rhinoplasty. Although the micro-endoscopic transnasal access is a more conservative technique, it allows greater surgical precision, and is currently recommended by many authors; choanal atresia repair is still considered a challenge, with risks of intraoperative and postoperative complications and re-stenosis. This paper reports the results of a series of 33 patients operated via the transnasal micro-endoscopic surgical approach, and describes a new endoscopic technique that the authors call "nasal septal crossover flap technique."