Background: The objective of the study is evaluation of ciliary function and mucosal cytology after endoscopic sinus surgery in children with chronic rhinosinusitis (CRS). Methodology: A total of 132 children with CRS who underwent endoscopic sinus surgery, as well as 15 healthy controls were involved in the study. In this follow-up study patients were examined preoperatively, as well as 3, 6, 9, and 12 months after endoscopic sinus surgery. Assessment of ciliary function and sinonasal mucosal cytology was performed using high-speed videomicroscopy. Lund-Kennedy, Lund-Mackay, and sinonasal outcome test 20 (SNOT20) scores were also evaluated. Results: Total SNOT-20, Lund-Mackay, and Lund-Kennedy values significantly decreased after sinus surgery. In contrast, ciliary function and mucosal cytology only tended to improve after 6 months. 9 months after surgery the number of ciliated cells, ciliary beat frequency, cell viability, and ciliary length were significantly higher than preoperatively. The most significant improvement of ciliary function and cell height was observed 12 months after operation, whereas epithelial dystrophy and neutrophil infiltration were significantly reduced. Conclusions: Substantial improvement was observed only in a year after surgery, whereas 0 to 3 months after the surgery ciliary function was severely impaired thus predisposing to recurrent sinusitis or other complications.