The Welfare Quality Assessment (WQA) was used in part of the Coalition for Sustainable Egg Supply (CSES) project to compare hens in three housing systems: aviary (AV), conventional cage (CC) and enriched colonies (EC). Lohmann LSL Classic White laying hens were placed in all three housing systems at 19 weeks of age and assessed at 52 and 72 weeks for the duration of two flocks. Evaluators used both the WQA and necropsies to assess welfare and found the WQA tool to be an acceptable method regarding hen welfare, as the results from both methods yielded similar results. AV and EC systems had more keel abnormalities and fewer foot abnormalities than CC houses. The overall feather cover was found to be the best in AV hens, although their feathers were the dirtiest.