Susceptibility of caged layers to osteoporosis and cage layer fatigue has generated interest in newer housing systems that favor increased load-bearing activities. However, high incidences of fractures incurred during lay period have been reported in these newer systems. This study is aimed at determining the housing and strain effects on bone properties: dry weight, percentage ash content, cortical density (CBD), cortical thickness (CBT), and keel bone deformities. Tibia, femur, and keel from Hy-Line Brown (HB), Hy-Line Silver Brown (SB), and Barred Plymouth Rock (BR) hens housed in conventional cages (CC), cage-free (CF), and cage-free with range (outdoor access; R) were studied. At 78 wk, 60 hens from each strain and housing system combination were euthanized and bones were excised for analysis. Quantitative computed tomography (QCT) was used to measure CBD and CBT in each bone. Three-dimensional images of keels were generated from software using QCT scans to analyze the deformities. Tibiae CBT was greater (P < 0.01) in BR compared to other two strains. Between housing systems, CBT was greater (P < 0.05) for mid and distal tibia of R and CF compared to CC. Tibiae and femoral cortex were denser (P < 0.05) in BR compared to HB and SB. There was no effect of housing system for femur CBD, but CBD was greater (P < 0.05) for middle and distal tibia of birds housed in R compared to CC. CBD for keel bone was greater (P < 0.05) in CF and R birds compared to CC birds. The housing system did not influence the dry bone weight and ash percentage of tibiae and femur. Each housing system was associated with high prevalence (>90%) of keel deformities and the housing and genotype influenced the type of deformity. These findings indicate that range and cage-free housing may have beneficial impact on tibia and keel bone integrity compared to conventional cages but the improvement may not be sufficient to prevent fractures or deformities of keel.