The bacterial eggshell contamination of eating eggs in different commercial housing systems; two conventional cages, one organic aviary system and one barn production, were compared. The total counts of aerobic bacteria and the total counts of Gram-negative bacteria on the shell were used to detect key points where contamination occurred and to study the progress of contamination in the egg collection and transportation chains. The key points in the chain were those where eggs accumulated on a short conveyor belt, initial shell contamination in the alternative housing systems and extra nest-boxes placed on the ground. The high bacterial load of floor eggs (>6.3 log CFU total aerobic flora/eggshell) explains why they cannot be used for eating. On average higher initial shell contamination with total counts of aerobic bacteria was found for eggs from the alternative housing systems compared to the conventional systems; respectively 5.46 compared to 5.08 log CFU/eggshell. However, initial contamination with total counts of Gram-negative bacteria on the shells was less in the alternative systems: 3.31 compared to 3.85 log CFU/shell. Initial bacterial shell contamination tended to correlate positively with the concentration of bacteria in the air of the poultry houses. Storing shell eggs, whether temporarily refrigerated or not, for 9 d or more, resulted in a decrease in bacterial eggshell contamination for both bacterial variables.