Technical Abstract: Alternative hen housing is becoming more commonplace in the egg market. However, a complete understanding of the implication of alternative housing systems on egg safety has not been achieved. The current study examines the impact of housing Hy-Line Brown, Hy-Line Silver Brown, and Barred Plymouth Rock hens in conventional cage, cage-free, and free range egg production systems on shell microbiology. Eggs were collected at four sampling periods. Egg shell emulsion pools were formed and enumerated for total aerobic organisms, Enterobacteriaceae, and yeast and mold counts. Hy-Line Brown and Hy-Line Silver Brown hens produced eggs with significantly (P < 0.05 and 0.001, respectively) different levels of aerobic organisms dependent on housing system. Eggs from conventional cages had significantly different (P < 0.05) levels of aerobic contaminations dependent on hen strain with Hy-Line Silver Brown having the greatest (4.57 log cfu/mL). Hy-Line Brown and Barred Plymouth Rock hens produced eggs with significantly different (P < 0.01) levels of Enterobacteriaceae amongst housing systems with conventional cage eggs having the lowest level of contamination for the hen strains. There were no differences within each strain amongst housing systems for yeast and mold contamination. The study shows that hen strain has a dynamic effect on egg microbial levels for various housing systems and egg safety should be considered when making hen strain selections for each housing system.