'Golden Delicious' apples taken from different points throughout the production chain and shelf-life were analysed for Enterobacteriaceae, thermotolerant coliforms, E. coli, E. coli O157:H7 and Salmonella spp. A total of 36 samples picked up in the orchard, 36 after storage and handling in the packinghouses and 144 from different retail stores were analysed using standardised techniques. Enterobacteriaceae counts were very variable. Pantoea spp. was the main genera isolated. The percentage of samples with thermotolerant coliforms was 16.6%, 22.2% and 10.4% after harvest, after handling in the packinghouse and in the stores, respectively. Strains belonging to Citrobacter, Enterobacter, Klebsiella and Escherichia were isolated. Three samples coming from orchards, five from the packinghouse and two from retailers harboured E. coli. However, none of the E. coli strains isolated had the virulence genes that are pathogenic for humans. None of the samples was Salmonella positive. This is the first study regarding microbial safety of fresh apples in the European Union (EU).