Objective. To analyze the effect of concomitant deviated nasal septum in children with chronic rhinosinusitis (CRS) on the effectiveness of functional endoscopic sinus surgery (FESS), the state of the ciliary apparatus, and the morphology of the nasal mucosa in the postoperative period. Patients and methods. A comprehensive examination was performed in 124 patients with CRS without nasal septum deviation as well as 66 patients with CRS and concomitant nasal septum deviation who underwent FESS. Results. A statistically significant improvement in the condition of the subjects after surgery was found in both groups. At the same time, patients with CRS and nasal septum deviation had a higher number of complications and the need for revision surgery. The subjective evaluation of the results of FESS was significantly higher in the group of children with CRS without nasal septum deviation. According to the results of video cytomorphometry in children with CRS without deviated nasal septum, by 6 and 12 months of the postoperative period, there was a close to significant and significant increase in the survival of epithelial cells, the number of cells with mobile cilia, the length of cilia, and the frequency of cilia beating. A year after the operation, this group of subjects also showed a statistically significant decrease in epithelial dystrophy, the number of neutrophils and lymphocytes, and a tendency to arrange cells in layers. In contrast, in patients with CRS and nasal septum deviation, a significant increase in the length of cilia was noted only by 12 months after surgery, while other parameters only tended to normalize. Synchronicity of cilia beat increased significantly by 12 months in both groups. Thus, the obtained results indicate a delayed recovery of the ciliary apparatus and the morphology of the ciliated epithelium mucosa after FESS in children with CRS and concomitant nasal septum deviation, which may be associated with persistent inflammation, causing a less favorable course of the postoperative period.