Inhalation of fungal spores is shown to participate in the development of allergic rhinitis symptoms. In this study, relation between presence of Alternaria in the human nasal cavity and allergic rhinitis is assessed. In a case-control study, 58 allergic rhinitis patients were compared with a well-matched control group of fifty healthy volunteers for sensitization to Alternaria (by skin prick test) and detection of Alternaria in their nasal mucous by conventional methods (microscopy with Methylene Blue stain and culture in Sabourad dextrose agar). Severity of the disease was determined according to the ARIA classification. Pearson chi-square test was applied to compare the proportional difference between the study groups for detection of Alternaria in the nasal cavity, and sensitization to Alternaria. Relation between detection of Alternaria and allergic rhinitis was significant [OR = 18.18 (4.02-82.50)] In addition, sensitization to Alternaria showed a significant relation with the disease [OR = 2.8 (2.1-3.8)]. There was a significant relation between the presence of Alternaria in the nasal cavity and sensitization to Alternaria [OR = 10.4 (3.8-28.3)]. Both sensitization to Alternaria and presence of Alternaria in the nasal cavity did not have a significant relation with the severity of allergic rhinitis. This study suggests Alternaria as a major allergen that its presence in the nasal cavity and subsequent development of sensitization have significant role in the induction of allergic rhinitis.