The current study sought to validate a proxy for egg laying that could be used within cage-free housing systems towards breeding programs of laying hens. Once validated, the proxy was then assessed against several common health and welfare traits (plumage, toe injuries, and body mass) to determine whether a relationship existed. We also estimated the heritabilities of the health traits and performed genome wide association studies to identify potential candidate gene, aiming to determine whether these phenotypes could be utilized in future breeding programs. Our effort used unique parental crosses with known pedigrees that allowed data within the cage free housing system to be compared with parallel family groups maintained in cages at the facility of our industrial partner. Findings indicated that the proxy of egg production was highly correlated with the production records of birds in cages. We also found that plumage in the cage-free housing system was positively related to the egg production proxy, whereas toe injuries were negatively related. We believe the findings support the position that phenotyping within cage-free housing systems can be a valuable component in efforts to breed hens that perform well in these systems.