The effect of functional endoscopic sinus surgery (FESS) was evaluated in 20 patients with chronic sinusitis. The physiological function of sinus mucosa and its mucociliary transport mechanism was assessed pre and post operatively in patients undergoing FESS by performing Saccharin clearance test. The effect of functional sinus surgery on nasal mucosa was evaluated using scanning electron microscopy and study of the ultrastructure of cilia in pre and post operative patients and correlation with histopathological examination. The mucociliary transport mechanism of the sinus mucosa improved 6 weeks following surgery. Histopathologically there was evidence of improvement in the ciliary population and decrease in inflammation, ulceration, fibrosis, vascular congestion, edema, squamous cell metaplasia, basement membrane thickening and polyp formation in comparison to the diseased mucosa sampled preoperatively. Scanning electron microscopic examination revealed considerable increase in the ciliary area as well as the orientation of cilia. Subjective improvement 6 weeks following surgery was confirmed by decrease in saccharin test time. This study revealed that FESS is an effective surgical procedure in chronic sinusitis and improves the overall function of the sinuses.