It has been described that influenza virus polymerase associates to the RNA polymerase II (RNAP II). To gain information about the role of this interaction, we explored if changes in RNAP II occur during infection. Here we show that influenza virus causes the specific degradation of the hypophosphorylated form of the largest subunit of the RNAP II without affecting the accumulation of its hyperphosphorylated forms. This effect is independent of the viral strain and the origin of the cells used. Analysis of synthesized mRNAs in isolated nuclei of infected cells indicated that transcription decreases concomitantly with the RNAP II degradation. Moreover, this degradation correlated with the onset of viral transcription and replication. The ubiquitin-mediated proteasome pathway is not involved in the viral-induced RNAP II proteolysis. The expression of the viral polymerase from its cloned cDNAs was sufficient to cause the degradation. Since PA polymerase subunit has proteolytic activity we tested its participation in the process. A recombinant virus with a PA point mutant with decreased proteolytic activity and defects in replication delayed the effect, suggesting its contribution to the RNA polymerase II degradation that occurs during the infection.