The contribution of fruit and vegetables to the burden of foodborne diseases has increased since the end of the eighties, stressing the need to control biological hazards in processed products. Salmonella, verotoxigenic Escherichia coli and foodborne viruses were the main pathogens transmitted by fruit, vegetables and product thereof, except for heat-treated products which mostly transmitted pathogenic Clostridium and Bacillus. Pathogenic Clostridium and Bacillus need to multiply to high numbers, or produce toxins, in the processed fruit and vegetables to cause diseases, in contrast to some Salmonella, verotoxigenic E. coli and viruses. Heat resistance of hepatitis A virus in fruits products is presented and compared to the stability of fruit enzymes such as PME. In the case of high hydrostatic pressure, the efficacy to kill E. coli and Salmonella in fruit and vegetables juices is strongly affected by the juice matrix. Challenge tests showed that botulinum toxin production is possible during refrigerated storage of heat processed vegetables, but the risk that it would occur in real conditions remains unknown. In the case of Bacillus cereus a recent reassessment of the phylogeny permitted to improve assessment of the risk in cooked chilled courgette purée.