Patulin is biosynthesized toxin produced by several species of filamentous fungi such as Penicillium spp., Aspergillus spp. and Byssochlamys nivea. The moulds grow on a variety of foods including fruits and fruit products. Patulin was recovered at different levels varied between 70-120%. The reproducibility expressed as relative standard deviation was less than 15%. The limit of quantification was 15µg/l. The method showed to be linear from the limit of quantification up to 200µg/L. The method accuracy was tested by participating in FAPAS proficiency test program. Forty-eight samples of clear apple juice collected from Egyptian local markets, half of these samples were from local production and the other imported from different countries. Patulin was detected in 22 out of 48 analyzed samples, at concentration levels ranged from 6.68 to 785.0 µg/L. The amount of patulin detected in 12 analyzed samples showed exceeding of permissible limit.