<b><i>Background:</i></b> Very few studies have investigated whether unilateral choanal atresia is associated with permanent olfactory deficits. <b><i>Objective:</i></b> This study aimed to evaluate the olfactory performance of patients with unilateral choanal atresia postsurgically. <b><i>Methods:</i></b> Three patients with unilateral atresia were examined in terms of olfactory performance with the Sniffin’ Sticks test (odor identification, threshold, and discrimination), size of the olfactory bulb, and volumetric brain changes. <b><i>Results:</i></b> All patients demonstrated significantly lower olfactory performance in terms of odor threshold on the same side with the choanal atresia. Grey matter reductions were found ipsilaterally in the hippocampus. <b><i>Conclusions:</i></b> This pilot study indicates that persistent olfactory deficits and volumetric brain changes are present in patients with unilateral choanal atresia.