Alternaria alternata (A. alternata) is one of the most common airborne fungi in outdoor and indoor environment. A. alternata has also considered as an aeroallergen. So, it could be responsible for an allergen release and may be responsible for allergic reactions in sensitive patients. The aim of this study was the analyzing of specific IgE against A. alternata in atopic dermatitis (AD) and asthma patients. A total of 50 AD patients (male 17 and female 33) and 50 asthma patients (male 20 and female 30) were entered in study. The range age vary from 4 months to 60 years. To analyzing of specific IgE, A. alternata was cultured in Sabouraud's dextrose agar. The grown fungi were harvested and ruptured by liquid nitrogen and glass beads. Samples were centrifuged at 3000rpm in 15 minutes and then at 15,500 rpm (4 degrees C) in 2 hours and then supernatant were collected as crude extract. The crude extract was separated by Sodium Dodecyl Sulfate-Polyacryl Amide Gel Electrophoresis (SDS-PAGE). The separated proteins transferred to nitrocellulose filter and then socked with atopic dermatitis and asthma patient's sera. The responsive bands to IgE were revealed by antihuman IgE antibodies conjugated with enzyme in chromogenic substrate. 16 (32%) and 19 (38%) of AD and asthma patients had specific IgE against A. alternata, respectively. Among the AD and asthma patients who were positive for specific IgE to A. alternata, 14 (87.5%) and 9 (47.4%) were women, respectively. Of the 16 AD patients for specific IgE positive, 9 (56.3%) were >12 years old. Of the 19 asthma patients for specific IgE positive, 10 (52.6%) were 20-39 years old. This study suggests that A. alternata is a major aeroallergen. Our previous studies as well as different studies from other countries have shown that A. alternata is one of the most common indoor and outdoor airborne fungi, so it could permanently present some allergens to susceptible individuals. Therefore, control of A. alternata growth in indoor areas and avoidance with A. alternata propagules could play an important role in reducing allergic reaction in susceptible individuals.