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Penicillium expansum is the principal cause of blue mould rot and associated production of patulin, a weak mycotoxin, in apples worldwide. P. expansum growth and patulin production is observed during improper or long-term storage of apples. We have investigated the extent to which each successive step during long-term storage contributes to patulin production in various P. expansum isolates. Fungal isolates collected on apples from several Belgian orchards/industries were identified to species level. Random amplification of polymorphic DNA (RAPD) analysis and β-tubulin gene sequencing identified P. expansum and Penicillium solitum as the most prevalent Penicillium species associated with Belgian apples. All 27 P. expansum isolates and eight reference strains were characterised for their patulin production capacity on apple puree agar medium for five days under classical constant temperature and atmosphere conditions. Under these conditions, a large range of patulin production levels was observed. Based on this phenotypic diversity, five P. expansum isolates and one reference strain were selected for in vitro investigation of patulin production under representative conditions in each step of long-term apple storage. Patulin accumulation seemed highly strain dependent and no significant differences between the storage steps were observed. The results also indicated that a high spore inoculum may lead to a strong patulin accumulation even at cold temperatures (1 °C) combined with controlled atmosphere (CA) (3% O2, 1% CO2), suggesting that future control strategies may benefit from considering the duration of storage under CA conditions as well as duration of deck storage.