Allergic diseases like atopic rhinitis, bronchial asthma, and urticaria are prevalent and on the rise. The need to better understand the pathophysiology of these diseases is therefore crucial to the development of newer and more effective modes of treatment. We hypothesized that in inflammatory diseases like allergic rhinitis and asthma characterized by profound local clinical manifestations and inflammation of the relevant mucosae, the most important immunopathological findings must occur locally. Although studies on the cellular elements and mediators in the peripheral blood compartment may provide useful information, they may not accurately reflect events occurring within the target organ itself. Even in the normal mucosa there is a resident population of lymphocytes and mast cells. Taking perennial allergic rhinitis (PAR) and chronic infective rhinitis (CIR) as representative chronic airway inflammatory diseases we investigated the phenotypic and functional characteristics of mast cells and lymphocytes in the nasal mucosa of patients with PAR and CIR during the natural course of the disease. We further compared the characteristics of lymphocytes in the nasal mucosa with that in the peripheral blood compartment. Our results demonstrated heterogeneity of mast cells and T cells in the nasal mucosa. Furthermore, the mucosal changes at the site of allergic inflammation were characterized by an increase in the proportion of CD4+ CD45RO+ T cells (memory cells); oligoclonal expansion and activation of V gamma 1/V delta 1+ T cells; an increased number of Fc epsilon RI+ cells; an increased proportion of TH2-type cytokine expressing mast cells and lymphocytes and of very late antigen-4 and very late antigen-5 expressing nasal mast cells, independent of alterations in CIR; and autologous peripheral blood. These findings strongly suggest heterogeneity of lymphocytes and mast cells in the nasal mucosa based on the underlying inflammatory disease, and compartmentalization of inflammatory cells in the nasal mucosa and peripheral blood.