Despite the varied immunological changes occurring after allergen immunotherapy, the precise mechanism, or the mechanisms responsible for clinical effectiveness of allergen immunotherapy have not been clearly determined. Postulated immunomodulatory mechanisms include a decrease in cellular responsiveness, a production of blocking antibodies, a reduction in the number of mast cells, and activation of T-cell suppressor mechanisms. Nineteen allergic rhinitis patients (study group) with house dust mite sensitivity and 10 nonallergic control subjects were studied. In the study group, the nasal mucosal biopsies were obtained prior to immunotherapy and were repeated after 1 year, and specimens were evaluated by light and electron microscopy. After the third month of immunotherapy, nasal symptom scores were reduced significantly and disappeared in the sixth month (p <0.01). No significant changes were observed in the levels of immunoglobulins, IgG subclasses and complement levels (p <0.05), except IgG4/IgG1 ratio (p <0.05). A comparison of histopathological findings of nasal mucosa in each case revealed an improvement in epithelial loss, inflammation, thickening of basal membrane and fibrosis (p <0.05). A significant correlation was observed between epithelial loss and mast cell accumulation with symptom score (p <0.001). These results suggest that the improvement of nasal epithelial cells and reduction of mast cell accumulation in nasal mucosa may be one of the mechanisms that could explain the improvement of nasal allergy symptoms following immunotherapy.