There is an overall trend in most of the developed countries that confirms the rise in the number of microbial contamination outbreaks associated with fresh products. Major contributing factors are global consumer demand, increasing worldwide trade and the development of new molecular tools that allow the identification of the causative agents and the outbreak traceability. This chapter examines the surveillance, source attribution and microbial risk assessment of foodborne pathogens. The chapter identifies the main sources for pathogen contamination, including primary production, processing, distribution, and cold chain. The chapter deals with the routes of pathogens contaminating fresh fruits and vegetables (FFV), as well as the factors affecting the survival or inactivation of pathogens in horticultural products. Finally, the chapter looks ahead to future research trends in this area.