Objective evaluation of mucociliary clearance and mucosal morphology using high-speed videomicroscopy, and their association with markers of disease severity in children with acute (ARS) and chronic rhinosinusitis (CRS). Methods A total of 67 children aged from 6 to 17 years including 15 healthy children, 20 pediatric patients with acute rhinosinusitis, and 32 cases with chronic rhinosinusitis were enrolled in the present study. SNOT20, Lund-Kennedy, and Lund-Mackay scores were also evaluated. Results Children with rhinosinusitis were characterized by significantly lower number of cells with motile cilia, ciliary beat frequency, cilia length, and cell viability, as well as ciliary beat asynchrony, epithelia dystrophy and reduced epithelial cell height, being more severe in ARS group. Neutrophil infiltration of sinonasal mucosa was more profound in children with ARS, whereas the number of lymphocytes was significantly reduced. Markers of ciliary function were characterized by a significant correlation with epithelia dystrophia and neutrophil infiltration. Discriminant analysis demonstrated significant group separation based on the parameters of mucociliary clearance and mucosal morphology. In regression models mucociliary function was also associated with SNOT20, Lund-Kennedy, and Lund-Mackay scores. Conclusion The results of the present study demonstrate significant alteration of mucociliary clearance and mucosal morphology and its association with sinonasal inflammation and disease severity in patients with rhinosinusitis. Given a tight association between altered mucociliary clearance and severity of the disease, modulation of inflammation and ciliary function both in acute and chronic rhinosinusitis may be considered as the potential tool in therapeutic and surgical management of the disease.