The purpose of this study was to identify the effects of long-term high comfort, low stress (HC) and low comfort, high stress (LC) housing environments milk quality, milk production, and immune function of Holstein dairy cattle. Thirty healthy, confirmed pregnant, lactating Holstein dairy cattle were selected from the University of Kentucky Dairy Research Herd and assigned to high comfort, low stress (n = 15) or low comfort, high stress (n = 15) environments for 28 d. After 28 d, cows were crossed-over to the alternate housing for an additional 28 d. Milk samples were collected every 7 d for SCC and culture, and milk production data were collected from the AfiLab (Afimilk, S.A.E. Afikim, Kibbutz Afikim, Israel). Blood samples were collected at the study’s beginning, midpoint, and end. Ten cows were selected from each sequence (10 HC to LC and 10 LC to HC) and blood samples stimulated with Escherichia coli 0111:B4 endotoxin, or left unstimulated as controls. Samples was lysed, RNA extracted, reverse transcribed, and cytokines quantified using PCR (IL-6, IL-8, IL-10, IFN-γ, and TNF-α). Individual cytokines, energy corrected milk, SCS, and subclinical infection prevalence were analyzed as dependent variables using mixed linear models in SAS (SAS Institute; Cary, NC). Housing type (HC or LC), sequence, and baseline values for each predicted variable served as fixed effects in each model. Cytokine models included treatment (endotoxin or unstimulated blood). Cow was a repeated subject in all models. All 2 and 3-way interactions were considered and non-significant (P ≥ 0.05) interactions removed using stepwise backward elimination. Housing type significantly affected ECM (LSmean ± SE; HC, 35.4 ± 0.4 vs. LC, 31.9 ± 0.9 kg) but not subclinical infection prevalence, SCS, or cytokine activity. Future analysis will include behavioral information from each cow and weather data. Stress in the housing environment did not affect immune function indicators but did decrease milk production.