Patulin, a secondary metabolite produced by Penicillium expansum and some other fungal species, is a common contaminant of ripened apples used for the production of apple juice concentrates. The limited availability of suitable storage facilities may result in fruit being subjected to storage in the open ('deck storage') for extended periods of time, prior to processing. A study was conducted to determine the influence that deck storage and subsequent initial processing practices had on patulin levels in freshly pressed juice. Over the study period, triplicate samples were collected at four strategic processing points from individual consignments of Granny Smith apples deck-stored for 7, 15 and 33 days, respectively. Over the study period, mean patulin levels in non-processed fruit increased from 90 to 2445 ng/g, respectively, but decreased to between 75 and 695 ng/g, respectively, following a water wash step. Subsequent removal of rotten/damaged fruit decreased patulin levels further (to between 55 and 405 ng/g, respectively), although the numerical decreases between sampling points were not shown to be statistically significant (P > 0.05). However, patulin levels were significantly higher (P < 0.05) in the rejected rotten/damaged fruit (mean levels ranged from 1120 to 6235 ng/g, respectively). P. expansum was the major patulin-producing fungus isolated from the juice samples. The mycological analyses tended to support the chemical data, in that removal of the rotten/damaged fractions significantly reduced total fungal counts in the juice samples.