Histopathological changes in septal and nasal mucosa of patients with nasal septum deviation are not well known. Biopsies of septal and lateral nasal mucosae from both sides of nose were obtained from 20 patients undergoing septoplasty and control group of 10 patients undergoing head and neck surgery. Histopathological changes including lymphocytic infiltration and squamous metaplasia were compared. This study determined significantly higher rate of squamous metaplasia and lymphocytic infiltration in septal mucosa opposite the deviation compared to control group. Furthermore, there was a significantly higher rate of lymphocytic infiltration in the lateral nasal wall mucosa opposite the deviation when compared to control group. Increased lymphocytic infiltration and squamous metaplasia are observed on both sides of nasal mucosa; however, they are more severe on the side opposite the deviation. Septal deviation predisposes to chronic mucosal inflammation and squamous metaplasia, both of which may render patients susceptible to chronic rhinosinusitis.