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In the country of Jordan, egg production is very important economically, but several bacte-ria are involved in food borne diseases transmitted from eggs or other poultry products. The most important are Salmonella spp., Campylobacter jejuni and Escherichia coli. In Jordan two different housing systems are used for hens in large scale egg production; con-ventional cages and litter floor systems. Eggs from four different farms were analysed and compared to see if a difference could be found regarding the presence of pathogenic bacte-ria on the egg surfaces between these two systems. Total number of aerobic bacteria was analysed, the presence of Salmonella spp., C. jejuni and E. coli, as well as the number of cracked eggs on the farms. Also air samples were taken in all systems and egg storage rooms. Our results showed significantly more pathogenic bacteria on eggs from the floor systems, both Salmonella spp. and E. coli. On the other hand, no significant difference could be detected in the amount of Campylobacter jejuni. The air samples showed more bacteria in the air of floor systems. Our conclusion is that eggs from hens in Jordanian floor systems are more contaminated with pathogenic bacteria than eggs from cage sys-tems.