Background: Fungal aeroallergens might sensitize the airway which in turn produces a specific cytokine profile. Objective: To evaluate the IL-25 and IL-33 profile in patients with fungal allergic rhinitis. Methods: The present study examined patients who were evaluated due to allergic rhinitis (AR) at Emam Reza Hospital of Shiraz, Iran. The allergic patients were categorized based on the skin prick test. Blood samples were collected and allergen-specific IgE and cytokine profiles were analyzed. Results: 184 patients were enrolled in the study and in 35 of whom fungal rhinitis was confirmed. The levels of specific IgE in patients with fungal allergy were statistically significant compared to those in the control group (p<0.000). However, there were no significant differences in IL-25 and IL-33 levels between fungal and none-fungal AR patients. Conclusion: Chronic fungal challenge might regulate innate system cytokines in severe persistent AR.