In the present study the global effect of restraint stress on gene expression in the murine lung during an experimental influenza A/PR8 viral infection was examined. Gene expression profiling using high density oligonucleotide microarrays revealed that the expression of 95 genes was altered on day 3 post infection (p.i.), while 48 genes were altered on day 7 p.i. Restraint stress reduced and delayed the expression of specific cytokines, cell adhesion molecules and cell surface receptors indicating alterations in cell migration to the site of infection. Furthermore, mapping of the candidate genes to known pathways revealed that genes associated with host defense and immune responses, including chemotaxis and chemokine function, antigen presentation and processing, MHC class II receptor function and inflammation were the major pathways affected by restraint stress.