Influenza A virus is a major cause of morbidity and mortality worldwide. There is a large knowledge base on the immune response to influenza. However, few studies have focused on global gene expression in immune cells after antigenic challenge. A better understanding of the host immune response is required for the development of more efficient means of prevention and treatment of influenza. In this study, global gene expression in peripheral blood mononuclear cells (PBMCs) after influenza immunization was analyzed. The differential gene expression in antigen-stimulated and non-stimulated PBMCs was determined by cDNA microarrays. To determine whether a specific gene profile was present during a proliferative memory cell response to influenza antigens, gene expression in response to PHA was compared with antigen-stimulated PBMCs. PHA induced the upregulation of 201 genes while influenza virus antigen upregulated more than triple that is 630 genes out of 1700 genes analyzed. Both influenza antigen and PHA commonly upregulated 138 genes. Interferon (IFN)-related genes were induced by influenza but not by PHA. The interferon-gamma induced protein precursor 10 (IP-10) was upregulated 27-fold while the interferon-induced 54 kDa protein exhibited a 13-fold increase. The following gene families were also selectively upregulated by influenza antigens: complement ligands and receptors, T cell activation genes, growth factors, genes related to antigen processing and inflammatory responses. With PHA, the genes TNF-R, CTSG, CD3 delta, C8B, CRF1 and CCR2 had higher expression compared with the viral antigen stimulation. Neutrophil defensins alpha-1 and two C-C chemokines, proteins MIP-1-beta and MIP-4, were among the genes upregulated by both PHA and influenza antigens. The results suggest that interferon-induced genes are one of the main transcriptional targets during the immune response to influenza virus.