Summary Objectives The aim of the study was to evaluate the effects of endoscopic sinus surgery for chronic maxillary sinusitis in children by investigating ultrastructure element changes in the sinus mucosa and nasal mucociliary clearance before and after operation. Methods Twenty-five children with chronic maxillary sinusitis scheduled to undergo functional endoscopic sinus surgery and another five controls were enrolled. A saccharin transit test was performed before and after the operation for each subject. Forty specimens of diseased maxillary sinus mucosa were classified into edematous and polypoid types, with 20 specimens in each type. The mucosal specimens were taken from the superolateral wall of each maxillary sinus during surgery and at post-operative follow-up when the mucosal recovery had begun and the symptoms had subsided. The specimens were examined with a scanning electron microscope. Results A significant increase in number of the submucosal gland openings (GO) was noted for the sinusitis group, of both edematous and polypoid types. In post-operative cases, the number of gland openings decreased, however, it remained higher than for the control group. The number of goblet cells (GC) decreased in the sinusitis cases, and significant difference was not demonstrated compared to postoperative and control groups. After endoscopic sinus surgery, the cilia in both types of antral mucosa were significantly regenerated compared to preoperative variants. Significant differences in postoperative saccharin transit time were demonstrated for both types of antral mucosa compared to the preoperative values. Conclusion After endoscopic sinus surgery for chronic pediatric sinusitis, the antral mucosa recovered and mucociliary clearance improved for both types of antral mucosa, with improved ventilation and drainage demonstrated for our patients. Based on our specimens, the edematous mucosa appear to regenerate sooner than the polypoid variant, with close post-operative follow-up for more than 2 and 4 months for the edematous and polypoid types of antral mucosa, respectively, necessary to prevent sinusitis relapse.