Contamination of vegetables and fruits is the result of presence of human pathogen bacteria which can contaminate products in any part of production chain. There is an evidence of presence of: Salmonella spp. on the fresh vegetables and Salmonellosis is connected with tomato, sprouts, cantaloupe etc. The goal of this research is transmission of pathogen bacteria from irrigation water to plants and studying/monitoring the ability of the Salmonella spp. to colonize the surface and interior (endophytic colonization) of root at different vegetable species. Transmission of three Salmonella spp. strains from irrigation water to plants, as well as colonization of plants by these bacteria was investigated by using Fluorescence In Situ Hybridization (FISH) in combination with confocal laser scanning microscopy (CLSM). All tested Salmonella spp. strains showed ability to more or less colonize the surface and interior niches of the root, stem and leaf of the investigated plant species. These bacteria also were found in plant cells cytoplasm, although the mechanism of their entrance has not been clarified yet.