Conditions for extraction and high-performance liquid chromatographic (HPLC) analysis for fourteen of the patulin pathway metabolites from Penicillium patulum are described which allow quantitation of the metabolite content of cultures at hourly intervals. The HPLC analysis is more sensitive than gas-liquid chromatographic analysis and is more quantitative than thin-layer chromatographic analysis. Separations on a preparative column allow for the collection and identification of new metabolites. The column elution program can be varied to optimize analysis time for individual metabolites, allowing individual enzymes of the pathway to be assayed by following the conversion of substrate to product. Analysis of product formation in crude enzyme mixtures can be used to assay an enzyme in the presence of subsequent enzymes of the pathway and to establish the pathway reaction sequence.