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The scientific community needs objective measures to appropriately assess animal welfare. The study objective was to assess the impact of housing system on novel physiological and behavioral measurements of animal welfare for laying hens, including secretory and plasma Immunoglobulin (IgA; immune function), feather corticosterone (chronic stress), and attention bias testing (ABT; anxiety), in addition to the well-validated tonic immobility test (TI; fearfulness). To test this, 184 Bovan brown hens were housed in 28 conventional cages (3 birds/cage) and 4 enriched pens (25 birds/pen). Feces, blood, and feathers were collected 4 times between week 22 and 43 to quantify secretory and plasma IgA and feather corticosterone concentrations. TI tests and ABT were performed once. Hens that were from cages tended to show longer TI, had increased feather corticosterone, and decreased secretory IgA at 22 weeks of age. The caged hens fed quicker, and more hens fed during the ABT compared to the penned hens. Hens that were in conventional cages showed somewhat poorer welfare outcomes than the hens in enriched pens, as indicated by increased chronic stress, decreased immune function at 22 weeks of age but no other ages, somewhat increased fear, but reduced anxiety. Overall, these novel markers show some appropriate contrast between housing treatments and may be useful in an animal welfare assessment context for laying hens. More research is needed to confirm these findings.