The aim the present study was the quantitative analysis of a potential fungal toxin, patulin in various samples of juice supplied from a commercial apple juice factory in Southwest area of Iran. For this purpose 150 samples of apple juice (local product) from the Southwest reign of Iran, were taken. Ten milliliter of each sample was dissolved in 5 mL buffer. The samples were treated by C18-SPE cartridge and analyzed by high-performance liquid chromatography (HPLC) using UV detector. Results showed level of patulin were higher than 10 μg L-1 in 90% of apple juices. Overall 13/3% of the apple juice samples had levels higher than 50 μg L-1 with maximum level of 106/01 μg L-1. The mean concentration of patulin in apple juice was 26/92 μg L-1. The results of this study showed not significant proportion of the patulin exceeding the 50 mg L-1 limit for apple juice set by WHO and certain European countries. However, constant surveillance of the patulin is strongly recommended because the available data is limited and the hot weather conditions in this area, incidence and level of this toxin could change according to factors like weather conditions, pH, type and stage of apple maturation. © 2010 Academic Journals Inc.