Choanal atresia (CA) is a congenital obstruction of the posterior nose. Bilateral CA is a paediatric emergency and must be treated surgically in the first few weeks after birth. This is in contrast to unilateral CA, because surgical management can be planned more selectively. Transpalatinal surgery for CA is a safe procedure. The endonasal technique is minimally invasive and less traumatic; however, a major disadvantage is a limited field of vision. Computer aided surgery using images acquired by computer tomography (CT) or magnetic resonance imaging (MRI) is an application that has emerged in the last few years. This application provides an additional safety factor for endoscopic surgery to resolve choanal atresia, especially in cases of another malformation. We report results from two cases of unilateral CA who were surgically managed with Computer aided surgery.