1. The welfare of hens in 26 flocks (6 conventional cage, 6 furnished cage, 7 barn, 7 free-range) was assessed throughout the laying period using a combination of data on physical health, physiology and injurious pecking, collected by researchers on farm and during post-mortem analysis, and information submitted by producers. 2. There was an effect of housing system on 5 of the indicators recorded by researchers: gentle feather pecks given, feather damage score, proportion of hens with feather damage, proportion of the flock using perches, and faecal corticosterone. 3. Post-mortem analysis revealed several differences between housing systems in skin damage, plumage damage to the vent and abdomen, keel protrusion, bodyweight, and the proportion of hens that were vent pecked and that had old and recent keel fractures. 4. There was an effect of housing system on 5 indicators recorded by producers: proportion of egg shells with calcification spots, proportion of egg shells with blood stains, weight of hens found dead, temporal change in the proportion of egg shells with stains, and temporal change in proportion of hens found dead. 5. Each housing system had positive and negative aspects but overall, hens in barn systems had the highest prevalence of poor plumage condition, old fractures, emaciation, abnormal egg calcification, and the highest corticosterone. Hens in conventional cages sustained more fractures at depopulation than birds in other systems. Vent pecking was most prevalent in free-range flocks. The lowest prevalence of problems occurred in hens in furnished cages. 6. Although housing system had an influence on the hens' physical condition and physiological state, the high prevalence of emaciation, loss of plumage, fractures and evidence of stress is of concern across all housing systems, and suggests that the welfare of modern genotypes is poor.