Laying hen welfare is gaining importance in the United States and several states have passed legislation for a welfare-friendly housing environment, which has forced the egg industry to explore alternative housing environments. For this reason, our first objective was to determine the effect of housing environment and laying hen strain on production performance and egg quality. Results showed that production performance of the hens raised in the alternative housing system was similar to the conventional system. The second objective was to compare the eggshell and cloacal microbiology. Our results indicated that the microbial load observed was higher in the alternative system compared to the conventional system. The third objective was to determine the effects of housing environment and laying hen strain on tibia and femur bone properties. The results demonstrated that the alternative system provided better tibia and femur bone characteristics, but it varied among laying hen strains.