A reliable method for the determination of patulin in apple juice, apple puree and apples was developed using two clean-up steps and high performance liquid chromatography and diode array (HPLC-DAD) analysis. Baseline separation from hydroxymethyl furfural (HMF) was obtained. The performance characteristics of the method were determined at four concentration levels in two matrices and fulfill the requirements of the European Commission (EC) for this type of samples. The level of quantification was set to 25 μg/l or 25 μg/kg, the RSD for repeatability at this level is 11% for apple juice and 17% for apples, the recovery is 87% for apple juice and 63% for apples. The reproducibility was determined in apples and is 11% (at a level of 200 μg/kg). The method was used for determination of patulin in 63 commercial apple products available on the Dutch market. With the exception of one sample, the level of patulin was lower than the detection limit in all the samples. No statistically significant difference was found between conventional and organic samples. © 2004 Elsevier Ltd. All rights reserved.