The effect of laying cycle, housing system and egg shell quality on microbial contamination of egg content was evaluated in ISA Brown hens housed in conventional cage and on litter. Eggs of laying hens housed in conventional cage and fed by mixture with 3.5 % of calcium had the highest quality of egg shell. Eggs from conventional cage were less penetrated by microorganisms contrary to litter. Lower microbial contamination was found out in eggs from hens in the first phase of laying cycle. Escherichia coli penetrated throught egg shell membrane earlier, after two days of storage. Whereas, penetration of enterococci into eggs was ascertained after seven days. Eggs from the second phase of laying cycle with the highest quality of egg shell were not penetrated by Escherichia coli and Enterococcus and also share of eggs contaminated by total count of microorganisms in the second and seventh day of storage was the lowest.