Interferon alpha (IFNalpha), produced primarily by plasmacytoid dendritic cells as part of the innate immune response to infectious agents, is a powerful polyclonal B-cell activator that induces a strong primary humoral immune response characterized by isotype switching and protection against virus challenge. IFNalpha has also been shown to stimulate an IgG2a antibody response characteristic of Th1 immunity when ad-mixed with influenza virus vaccine. The use of transgenic mice expressing a green fluorescent protein reporter gene regulated by an IFN responsive element has shown that IFN-activated cells are present in the peripheral circulation of influenza vaccinated mice as early as 4 h after initiation of IFNalpha treatment and that the principal cell populations activated by IFN treatment included B220 (-) Ly6c (-), CD11c (high), CD11b (high), CD8 (+) cells, and B220 (high), Ly6c (high), CD11c (low), CD11b (-), CD4 (+), CD19 (-) cells. The effect of IFNalpha on the antibody response to influenza vaccination was shown to be dependent upon the route of administration. Differential display analysis showed that numerous IFN responsive genes were induced in the lymphoid tissue of IFN treated animals together with a number of genes not previously shown to be induced by IFNalpha including Crg2 and other chemokines, proteases associated with antigen processing, and genes involved in lymphocyte activation, apoptosis, and protein degradation. Together these results may explain in part the mechanism(s) of the adjuvant activity of IFNalpha.