Specific ultrastructural findings have widely been described in case of obstructive nasal diseases due to congenital defects. Ciliary impairment has in particular been observed as the main pathological feature in these conditions. In this study, nasal mucosal samples from different pathologies have been collected via the "brushing" technique and analysed by transmission electron microscopy. TEM analysis was focused on specific features, such as the numerical array of peripheral and central doublets of the cilium axoneme, including eventual microtubular disarrangement; partial or total loss of inner and/or outer dynein arms; defects of radial spokes and nexin links; disorientation of the ciliary axis in closely adjacent cilia, calculating the angle between the line crossing the central microtubular core and the horizontal ciliary axis and compound cilia (CC). Statistical comparison was carried out between study and control groups. A significant incidence of organic ciliary defects was found not only in patients with inflammatory processes, but mostly in those supposed to have a long-lasting nasal respiratory disease due to mechanical stenosis in relation to septum deviation and turbinate hypertrophy. Prevalence and percentage of compound cilia were instead more related to inflammatory conditions. The "brushing" technique can be considered an easy and reliable method for the assessment of the condition of the nasal mucosa. According to the findings derived from this study, mechanical nasal obstruction seems to cause major alterations on the nasal ciliary arrangement, thus determining a functional impairment on the whole nasal function.