The Welfare Quality® Assessment protocol for poultry (WQA) provides animal-based measures allowing welfare comparisons across farms and housing systems. It was used to compare Lohmann LSL Classic White hens housed in an enriched colony (EC), aviary (AV), and conventional cage system (CC) on a commercial farm over 2 flock cycles. Hens (n = 100/system) were scored on a variety of measures. A baseline measurement was made at placement at 19 wk of age for 1 flock, since AV hens had been reared in an aviary pullet facility (AVP) while EC and CC hens were reared in a conventional pullet facility (CCP). Hens in all systems were then assessed at 52 and 72 wk of age. Necropsies were performed on all mortalities 1 wk before and after the WQA sampling. WQAs were analyzed using Mann–Whitney U and Kruskal–Wallis tests for prevalence and Fisher's exact tests for severity. There was an effect of rearing, with AVP having shorter claws (P = 0.01), dirtier feathers (P = 0.03), and more keel abnormalities (P < 0.0001) than CCP at placement. For the hens, there were several significant housing system effects across flocks and age periods (all P ≤ 0.05). AV and EC hens had more keel abnormalities than CC hens. They also had fewer foot abnormalities than CC hens, although those in AV hens were more severe. AV hens had consistently dirtier feathers than EC and CC hens. While AV hens had the best overall feather cover, feather loss patterns suggested that loss was due to head pecking for AV, whereas in EC and CC it was due to cage abrasion. The necropsy findings and the WQA results were similar, except that the WQA failed to find enteritis at 19 wk, although it was detected in the necropsies during this sampling period. These results show that the WQA is a useful tool for detecting hen condition differences across housing systems.